diff --git a/404.html b/404.html
index 3ed330c..acaf5b7 100644
--- a/404.html
+++ b/404.html
@@ -14,15 +14,12 @@
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
 <meta property="og:title" content="Page not found (404)">
 <meta property="og:image" content="/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -32,69 +29,46 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul>
 </li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="logo.png" class="logo" alt=""><h1>Page not found (404)</h1>
-      
+
     </div>
 
 Content not found. Please use links in the navbar.
@@ -108,15 +82,15 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index d9da739..7d1cd03 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="License"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="License"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="logo.png" class="logo" alt=""><h1>License</h1>
-      
+
     </div>
 
 <pre>                    GNU GENERAL PUBLIC LICENSE
@@ -754,14 +727,14 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/articles/MOFA_to_COSMOS.html b/articles/MOFA_to_COSMOS.html
index 75b9b3f..04276cf 100644
--- a/articles/MOFA_to_COSMOS.html
+++ b/articles/MOFA_to_COSMOS.html
@@ -5,7 +5,6 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="cosmosR">
 <title>MOFA to COSMOS tutorial • cosmosR</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
@@ -15,16 +14,11 @@
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="MOFA to COSMOS tutorial">
-<meta property="og:description" content="cosmosR">
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-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
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   gtag('js', new Date());
@@ -34,63 +28,40 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul>
 </li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -102,7 +73,7 @@
       <img src="../logo.png" class="logo" alt=""><h1>MOFA to COSMOS tutorial</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/vignettes/MOFA_to_COSMOS.Rmd" class="external-link"><code>vignettes/MOFA_to_COSMOS.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/vignettes/MOFA_to_COSMOS.Rmd" class="external-link"><code>vignettes/MOFA_to_COSMOS.Rmd</code></a></small>
       <div class="d-none name"><code>MOFA_to_COSMOS.Rmd</code></div>
     </div>
 
@@ -1557,7 +1528,7 @@ <h3 id="session-info">Session info</h3>
 <span><span class="co">## [159] blob_1.2.3                  textshaping_0.3.6          </span></span>
 <span><span class="co">## [161] BiocSingular_1.12.0         memoise_2.0.1              </span></span>
 <span><span class="co">## [163] irlba_2.3.5.1               future.apply_1.10.0</span></span></code></pre>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -1568,15 +1539,15 @@ <h3 id="session-info">Session info</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/articles/NCI60_tutorial.html b/articles/NCI60_tutorial.html
index 9152989..6ea0b6a 100644
--- a/articles/NCI60_tutorial.html
+++ b/articles/NCI60_tutorial.html
@@ -5,7 +5,6 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="cosmosR">
 <title>NCI60 tutorial • cosmosR</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
@@ -15,16 +14,11 @@
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 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="NCI60 tutorial">
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-<meta property="og:image" content="/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -34,63 +28,40 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
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-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
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-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul>
 </li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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-  <a class="external-link nav-link" href="https://saezlab.org">
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-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
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 </div>
 
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 </nav><div class="container template-article">
 
@@ -102,7 +73,7 @@
       <img src="../logo.png" class="logo" alt=""><h1>NCI60 tutorial</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/vignettes/NCI60_tutorial.Rmd" class="external-link"><code>vignettes/NCI60_tutorial.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/vignettes/NCI60_tutorial.Rmd" class="external-link"><code>vignettes/NCI60_tutorial.Rmd</code></a></small>
       <div class="d-none name"><code>NCI60_tutorial.Rmd</code></div>
     </div>
 
@@ -336,7 +307,7 @@ <h2 id="run-moon-ot-score-the-and-contextualise-the-pkn">run MOON ot score the a
 <span><span class="co">## [41] tzdb_0.3.0        tidyr_1.3.0       purrr_1.0.1       decoupleR_2.9.1  </span></span>
 <span><span class="co">## [45] magrittr_2.0.3    htmltools_0.5.5   utf8_1.2.3        stringi_1.7.12   </span></span>
 <span><span class="co">## [49] crayon_1.5.2</span></span></code></pre>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -347,15 +318,15 @@ <h2 id="run-moon-ot-score-the-and-contextualise-the-pkn">run MOON ot score the a
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/articles/index.html b/articles/index.html
index 2e2b0e4..d3de856 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Articles"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Articles"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,58 +7,34 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-article-index">
 <div class="row">
@@ -88,14 +61,14 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/articles/tutorial.html b/articles/tutorial.html
index ca7c146..361a66c 100644
--- a/articles/tutorial.html
+++ b/articles/tutorial.html
@@ -5,7 +5,6 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="cosmosR">
 <title>COSMOS-tutorial • cosmosR</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
@@ -15,16 +14,11 @@
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <meta property="og:title" content="COSMOS-tutorial">
-<meta property="og:description" content="cosmosR">
-<meta property="og:image" content="/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -34,63 +28,40 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="active nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul>
 </li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-article">
 
@@ -105,7 +76,7 @@ <h4 data-toc-skip class="author">A. Dugourd, A.
             
             <h4 data-toc-skip class="date">11/10/2020</h4>
       
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/vignettes/tutorial.Rmd" class="external-link"><code>vignettes/tutorial.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/vignettes/tutorial.Rmd" class="external-link"><code>vignettes/tutorial.Rmd</code></a></small>
       <div class="d-none name"><code>tutorial.Rmd</code></div>
     </div>
 
@@ -465,7 +436,7 @@ <h2 id="tutorial-section-over-representation-analysis">Tutorial section: Over Re
 analysis.</p>
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## R version 4.4.0 (2024-04-24)</span></span>
+<pre><code><span><span class="co">## R version 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu</span></span>
 <span><span class="co">## Running under: Ubuntu 22.04.4 LTS</span></span>
 <span><span class="co">## </span></span>
@@ -494,28 +465,27 @@ <h2 id="tutorial-section-over-representation-analysis">Tutorial section: Over Re
 <span><span class="co">##  [1] bcellViper_1.40.0   sass_0.4.9          utf8_1.2.4         </span></span>
 <span><span class="co">##  [4] generics_0.1.3      tidyr_1.3.1         lpSolve_5.6.20     </span></span>
 <span><span class="co">##  [7] stringi_1.8.4       lattice_0.22-6      hms_1.1.3          </span></span>
-<span><span class="co">## [10] digest_0.6.35       magrittr_2.0.3      evaluate_0.24.0    </span></span>
-<span><span class="co">## [13] grid_4.4.0          fastmap_1.2.0       jsonlite_1.8.8     </span></span>
+<span><span class="co">## [10] digest_0.6.36       magrittr_2.0.3      evaluate_0.24.0    </span></span>
+<span><span class="co">## [13] grid_4.4.1          fastmap_1.2.0       jsonlite_1.8.8     </span></span>
 <span><span class="co">## [16] Matrix_1.7-0        progress_1.2.3      purrr_1.0.2        </span></span>
 <span><span class="co">## [19] fansi_1.0.6         codetools_0.2-20    textshaping_0.4.0  </span></span>
 <span><span class="co">## [22] jquerylib_0.1.4     cli_3.6.3           rlang_1.1.4        </span></span>
 <span><span class="co">## [25] decoupleR_2.10.0    crayon_1.5.3        visNetwork_2.1.2   </span></span>
 <span><span class="co">## [28] parallelly_1.37.1   bit64_4.0.5         withr_3.0.0        </span></span>
-<span><span class="co">## [31] cachem_1.1.0        yaml_2.3.8          tools_4.4.0        </span></span>
-<span><span class="co">## [34] parallel_4.4.0      tzdb_0.4.0          BiocParallel_1.38.0</span></span>
-<span><span class="co">## [37] memoise_2.0.1       dplyr_1.1.4         vctrs_0.6.5        </span></span>
-<span><span class="co">## [40] R6_2.5.1            lifecycle_1.0.4     stringr_1.5.1      </span></span>
-<span><span class="co">## [43] bit_4.0.5           fs_1.6.4            htmlwidgets_1.6.4  </span></span>
-<span><span class="co">## [46] vroom_1.6.5         ragg_1.3.2          pkgconfig_2.0.3    </span></span>
-<span><span class="co">## [49] desc_1.4.3          pkgdown_2.0.9       pillar_1.9.0       </span></span>
-<span><span class="co">## [52] bslib_0.7.0         glue_1.7.0          systemfonts_1.1.0  </span></span>
-<span><span class="co">## [55] xfun_0.45           tibble_3.2.1        tidyselect_1.2.1   </span></span>
-<span><span class="co">## [58] CARNIVAL_2.14.0     knitr_1.47          dorothea_1.16.0    </span></span>
-<span><span class="co">## [61] rjson_0.2.21        igraph_2.0.3        htmltools_0.5.8.1  </span></span>
-<span><span class="co">## [64] rmarkdown_2.27      readr_2.1.5         compiler_4.4.0     </span></span>
-<span><span class="co">## [67] prettyunits_1.2.0</span></span></code></pre>
+<span><span class="co">## [31] cachem_1.1.0        yaml_2.3.9          tools_4.4.1        </span></span>
+<span><span class="co">## [34] parallel_4.4.1      tzdb_0.4.0          BiocParallel_1.38.0</span></span>
+<span><span class="co">## [37] dplyr_1.1.4         vctrs_0.6.5         R6_2.5.1           </span></span>
+<span><span class="co">## [40] lifecycle_1.0.4     stringr_1.5.1       bit_4.0.5          </span></span>
+<span><span class="co">## [43] fs_1.6.4            htmlwidgets_1.6.4   vroom_1.6.5        </span></span>
+<span><span class="co">## [46] ragg_1.3.2          pkgconfig_2.0.3     desc_1.4.3         </span></span>
+<span><span class="co">## [49] pkgdown_2.1.0       pillar_1.9.0        bslib_0.7.0        </span></span>
+<span><span class="co">## [52] glue_1.7.0          systemfonts_1.1.0   xfun_0.45          </span></span>
+<span><span class="co">## [55] tibble_3.2.1        tidyselect_1.2.1    knitr_1.48         </span></span>
+<span><span class="co">## [58] CARNIVAL_2.14.0     dorothea_1.16.0     rjson_0.2.21       </span></span>
+<span><span class="co">## [61] igraph_2.0.3        htmltools_0.5.8.1   rmarkdown_2.27     </span></span>
+<span><span class="co">## [64] readr_2.1.5         compiler_4.4.1      prettyunits_1.2.0</span></span></code></pre>
 </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
 </div>
 
@@ -526,15 +496,15 @@ <h2 id="tutorial-section-over-representation-analysis">Tutorial section: Over Re
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
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 </div>
 
-  
 
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diff --git a/authors.html b/authors.html
index 520ad58..424ebc9 100644
--- a/authors.html
+++ b/authors.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,58 +7,34 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-citation-authors">
 <div class="row">
@@ -69,9 +42,9 @@
       <img src="logo.png" class="logo" alt=""><h1>Authors and Citation</h1>
     </div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2>Authors</h2>
-      
+
       <ul class="list-unstyled"><li>
           <p><strong>Aurélien Dugourd</strong>. Author. <a href="https://orcid.org/0000-0002-0714-028X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
@@ -86,9 +59,9 @@ <h2>Authors</h2>
         </li>
       </ul></div>
 
-    <div class="section level2 citation">
+    <div class="section level2">
       <h2 id="citation">Citation</h2>
-      <p><small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
 
       <p>Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B. Emdal, Vitor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric. M. J. Bindels, Ana S. H. Costa, Abel sousa, Pedro Beltrao, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez. 'Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.' Molecular Systems Biology. 2021.</p>
       <pre>@Article{,
@@ -98,7 +71,8 @@ <h2 id="citation">Citation</h2>
   year = {2021},
 }</pre>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -107,14 +81,14 @@ <h2 id="citation">Citation</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
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diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
index fe691ba..016476c 100644
--- a/deps/bootstrap-5.3.1/bootstrap.min.css
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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #373a3c;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #285FA9;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(40,95,169,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: var(--bs-border-color);--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width))}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #285FA9}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(255,255,255,0.65);--bs-navbar-hover-color: rgba(0,0,0,0.9);--bs-navbar-disabled-color: rgba(255,255,255,0.3);--bs-navbar-active-color: #fff;--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: #fff;--bs-navbar-brand-hover-color: #fff;--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(255,255,255,0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) var(--bs-navbar-padding-x)}.navbar>.container,.navbar>.container-fluid,.navbar>.container-sm,.navbar>.container-md,.navbar>.container-lg,.navbar>.container-xl,.navbar>.container-xxl{display:flex;display:-webkit-flex;flex-wrap:inherit;-webkit-flex-wrap:inherit;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between}.navbar-brand{padding-top:var(--bs-navbar-brand-padding-y);padding-bottom:var(--bs-navbar-brand-padding-y);margin-right:var(--bs-navbar-brand-margin-end);font-size:var(--bs-navbar-brand-font-size);color:var(--bs-navbar-brand-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;white-space:nowrap}.navbar-brand:hover,.navbar-brand:focus{color:var(--bs-navbar-brand-hover-color)}.navbar-nav{--bs-nav-link-padding-x: 0;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-navbar-color);--bs-nav-link-hover-color: var(--bs-navbar-hover-color);--bs-nav-link-disabled-color: var(--bs-navbar-disabled-color);display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;list-style:none}.navbar-nav .nav-link.active,.navbar-nav .nav-link.show{color:var(--bs-navbar-active-color)}.navbar-nav .dropdown-menu{position:static}.navbar-text{padding-top:.5rem;padding-bottom:.5rem;color:var(--bs-navbar-color)}.navbar-text a,.navbar-text a:hover,.navbar-text a:focus{color:var(--bs-navbar-active-color)}.navbar-collapse{flex-basis:100%;-webkit-flex-basis:100%;flex-grow:1;-webkit-flex-grow:1;align-items:center;-webkit-align-items:center}.navbar-toggler{padding:var(--bs-navbar-toggler-padding-y) var(--bs-navbar-toggler-padding-x);font-size:var(--bs-navbar-toggler-font-size);line-height:1;color:var(--bs-navbar-color);background-color:transparent;border:var(--bs-border-width) solid 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.nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-sm .navbar-nav-scroll{overflow:visible}.navbar-expand-sm .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-sm .navbar-toggler{display:none}.navbar-expand-sm .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-sm .offcanvas .offcanvas-header{display:none}.navbar-expand-sm .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 768px){.navbar-expand-md{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-md .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-md .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-md .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-md .navbar-nav-scroll{overflow:visible}.navbar-expand-md .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-md .navbar-toggler{display:none}.navbar-expand-md .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-md .offcanvas .offcanvas-header{display:none}.navbar-expand-md .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1200px){.navbar-expand-xl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xl .navbar-nav-scroll{overflow:visible}.navbar-expand-xl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xl .navbar-toggler{display:none}.navbar-expand-xl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand .navbar-toggler{display:none}.navbar-expand .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme="dark"]{--bs-navbar-color: rgba(255,255,255,0.55);--bs-navbar-hover-color: #fff;--bs-navbar-disabled-color: rgba(255,255,255,0.25);--bs-navbar-active-color: #fff;--bs-navbar-brand-color: #fff;--bs-navbar-brand-hover-color: #fff;--bs-navbar-toggler-border-color: rgba(255,255,255,0.1);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: var(--bs-body-bg);--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card>hr{margin-right:0;margin-left:0}.card>.list-group{border-top:inherit;border-bottom:inherit}.card>.list-group:first-child{border-top-width:0}.card>.list-group:last-child{border-bottom-width:0}.card>.card-header+.list-group,.card>.list-group+.card-footer{border-top:0}.card-body{flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-card-spacer-y) var(--bs-card-spacer-x);color:var(--bs-card-color)}.card-title{margin-bottom:var(--bs-card-title-spacer-y);color:var(--bs-card-title-color)}.card-subtitle{margin-top:calc(-.5 * var(--bs-card-title-spacer-y));margin-bottom:0;color:var(--bs-card-subtitle-color)}.card-text:last-child{margin-bottom:0}.card-link+.card-link{margin-left:var(--bs-card-spacer-x)}.card-header{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);margin-bottom:0;color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-bottom:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-footer{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-top:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-header-tabs{margin-right:calc(-.5 * var(--bs-card-cap-padding-x));margin-bottom:calc(-1 * var(--bs-card-cap-padding-y));margin-left:calc(-.5 * var(--bs-card-cap-padding-x));border-bottom:0}.card-header-tabs .nav-link.active{background-color:var(--bs-card-bg);border-bottom-color:var(--bs-card-bg)}.card-header-pills{margin-right:calc(-.5 * 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calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23373a3c'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23102644'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 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var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:not(:first-of-type){border-top:0}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237e9fcb'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237e9fcb'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(40,95,169,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #285FA9;--bs-pagination-active-border-color: #285FA9;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 0 solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:.5rem}}.progress,.progress-stacked{--bs-progress-height: .5rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #285FA9;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #285FA9;--bs-list-group-active-border-color: #285FA9;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(40,95,169,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 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#fff;--bs-dropdown-link-active-bg: #285FA9;--bs-dropdown-link-disabled-color: var(--bs-tertiary-color);--bs-dropdown-item-padding-x: 1rem;--bs-dropdown-item-padding-y: .25rem;--bs-dropdown-header-color: #868e96;--bs-dropdown-header-padding-x: 1rem;--bs-dropdown-header-padding-y: .5rem;position:absolute;z-index:var(--bs-dropdown-zindex);display:none;min-width:var(--bs-dropdown-min-width);padding:var(--bs-dropdown-padding-y) var(--bs-dropdown-padding-x);margin:0;font-size:var(--bs-dropdown-font-size);color:var(--bs-dropdown-color);text-align:left;list-style:none;background-color:var(--bs-dropdown-bg);background-clip:padding-box;border:var(--bs-dropdown-border-width) solid var(--bs-dropdown-border-color)}.dropdown-menu[data-bs-popper]{top:100%;left:0;margin-top:var(--bs-dropdown-spacer)}.dropdown-menu-start{--bs-position: start}.dropdown-menu-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-end{--bs-position: end}.dropdown-menu-end[data-bs-popper]{right:0;left:auto}@media (min-width: 576px){.dropdown-menu-sm-start{--bs-position: start}.dropdown-menu-sm-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-sm-end{--bs-position: end}.dropdown-menu-sm-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 768px){.dropdown-menu-md-start{--bs-position: start}.dropdown-menu-md-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-md-end{--bs-position: end}.dropdown-menu-md-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 992px){.dropdown-menu-lg-start{--bs-position: start}.dropdown-menu-lg-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-lg-end{--bs-position: end}.dropdown-menu-lg-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1200px){.dropdown-menu-xl-start{--bs-position: start}.dropdown-menu-xl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xl-end{--bs-position: end}.dropdown-menu-xl-end[data-bs-popper]{right:0;left:auto}}@media (min-width: 1400px){.dropdown-menu-xxl-start{--bs-position: 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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #373a3c;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #285FA9;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(40,95,169,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: 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var(--bs-navbar-hover-color);--bs-nav-link-disabled-color: var(--bs-navbar-disabled-color);display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;list-style:none}.navbar-nav .nav-link.active,.navbar-nav .nav-link.show{color:var(--bs-navbar-active-color)}.navbar-nav .dropdown-menu{position:static}.navbar-text{padding-top:.5rem;padding-bottom:.5rem;color:var(--bs-navbar-color)}.navbar-text a,.navbar-text a:hover,.navbar-text a:focus{color:var(--bs-navbar-active-color)}.navbar-collapse{flex-basis:100%;-webkit-flex-basis:100%;flex-grow:1;-webkit-flex-grow:1;align-items:center;-webkit-align-items:center}.navbar-toggler{padding:var(--bs-navbar-toggler-padding-y) var(--bs-navbar-toggler-padding-x);font-size:var(--bs-navbar-toggler-font-size);line-height:1;color:var(--bs-navbar-color);background-color:transparent;border:var(--bs-border-width) solid 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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.offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme="dark"] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: var(--bs-border-width);--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: var(--bs-border-radius);--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: var(--bs-body-bg);--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card>hr{margin-right:0;margin-left:0}.card>.list-group{border-top:inherit;border-bottom:inherit}.card>.list-group:first-child{border-top-width:0}.card>.list-group:last-child{border-bottom-width:0}.card>.card-header+.list-group,.card>.list-group+.card-footer{border-top:0}.card-body{flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-card-spacer-y) var(--bs-card-spacer-x);color:var(--bs-card-color)}.card-title{margin-bottom:var(--bs-card-title-spacer-y);color:var(--bs-card-title-color)}.card-subtitle{margin-top:calc(-.5 * var(--bs-card-title-spacer-y));margin-bottom:0;color:var(--bs-card-subtitle-color)}.card-text:last-child{margin-bottom:0}.card-link+.card-link{margin-left:var(--bs-card-spacer-x)}.card-header{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);margin-bottom:0;color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-bottom:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-footer{padding:var(--bs-card-cap-padding-y) var(--bs-card-cap-padding-x);color:var(--bs-card-cap-color);background-color:var(--bs-card-cap-bg);border-top:var(--bs-card-border-width) solid var(--bs-card-border-color)}.card-header-tabs{margin-right:calc(-.5 * var(--bs-card-cap-padding-x));margin-bottom:calc(-1 * var(--bs-card-cap-padding-y));margin-left:calc(-.5 * var(--bs-card-cap-padding-x));border-bottom:0}.card-header-tabs .nav-link.active{background-color:var(--bs-card-bg);border-bottom-color:var(--bs-card-bg)}.card-header-pills{margin-right:calc(-.5 * var(--bs-card-cap-padding-x));margin-left:calc(-.5 * var(--bs-card-cap-padding-x))}.card-img-overlay{position:absolute;top:0;right:0;bottom:0;left:0;padding:var(--bs-card-img-overlay-padding)}.card-img,.card-img-top,.card-img-bottom{width:100%}.card-group>.card{margin-bottom:var(--bs-card-group-margin)}@media (min-width: 576px){.card-group{display:flex;display:-webkit-flex;flex-flow:row wrap;-webkit-flex-flow:row wrap}.card-group>.card{flex:1 0 0%;-webkit-flex:1 0 0%;margin-bottom:0}.card-group>.card+.card{margin-left:0;border-left:0}}.accordion{--bs-accordion-color: var(--bs-body-color);--bs-accordion-bg: var(--bs-body-bg);--bs-accordion-transition: color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out,border-radius 0.15s ease;--bs-accordion-border-color: var(--bs-border-color);--bs-accordion-border-width: var(--bs-border-width);--bs-accordion-border-radius: var(--bs-border-radius);--bs-accordion-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-accordion-btn-padding-x: 1.25rem;--bs-accordion-btn-padding-y: 1rem;--bs-accordion-btn-color: var(--bs-body-color);--bs-accordion-btn-bg: var(--bs-accordion-bg);--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23373a3c'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-icon-width: 1.25rem;--bs-accordion-btn-icon-transform: rotate(-180deg);--bs-accordion-btn-icon-transition: transform 0.2s ease-in-out;--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23102644'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #94afd4;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(40,95,169,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:not(:first-of-type){border-top:0}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237e9fcb'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237e9fcb'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(40,95,169,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #285FA9;--bs-pagination-active-border-color: #285FA9;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 0 solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:.5rem}}.progress,.progress-stacked{--bs-progress-height: .5rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #285FA9;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #285FA9;--bs-list-group-active-border-color: #285FA9;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(40,95,169,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color)}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y) * .5) calc(var(--bs-modal-header-padding-x) * .5);margin:calc(-.5 * var(--bs-modal-header-padding-y)) calc(-.5 * var(--bs-modal-header-padding-x)) calc(-.5 * var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap) * .5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap) * .5)}@media (min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media (min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media (min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0}.modal-fullscreen .modal-body{overflow-y:auto}@media (max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media (max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media (max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media (max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: .5rem;--bs-tooltip-padding-y: .25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: .9;--bs-tooltip-arrow-width: .8rem;--bs-tooltip-arrow-height: .4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow{left:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow{top:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: var(--bs-border-color-translucent);--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: .5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: .5rem;--bs-popover-arrow-border: 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diff --git a/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js b/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
new file mode 100644
index 0000000..c628326
--- /dev/null
+++ b/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap Table of Contents v1.0.1 (http://afeld.github.io/bootstrap-toc/)
+ * Copyright 2015 Aidan Feldman
+ * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
+!function(a){"use strict";window.Toc={helpers:{findOrFilter:function(e,t){var n=e.find(t);return e.filter(t).add(n).filter(":not([data-toc-skip])")},generateUniqueIdBase:function(e){return a(e).text().trim().replace(/\'/gi,"").replace(/[& +$,:;=?@"#{}|^~[`%!'<>\]\.\/\(\)\*\\\n\t\b\v]/g,"-").replace(/-{2,}/g,"-").substring(0,64).replace(/^-+|-+$/gm,"").toLowerCase()||e.tagName.toLowerCase()},generateUniqueId:function(e){for(var t=this.generateUniqueIdBase(e),n=0;;n++){var r=t;if(0<n&&(r+="-"+n),!document.getElementById(r))return r}},generateAnchor:function(e){if(e.id)return e.id;var t=this.generateUniqueId(e);return e.id=t},createNavList:function(){return a('<ul class="nav navbar-nav"></ul>')},createChildNavList:function(e){var t=this.createNavList();return e.append(t),t},generateNavEl:function(e,t){var n=a('<a class="nav-link"></a>');n.attr("href","#"+e),n.text(t);var r=a("<li></li>");return r.append(n),r},generateNavItem:function(e){var t=this.generateAnchor(e),n=a(e),r=n.data("toc-text")||n.text();return this.generateNavEl(t,r)},getTopLevel:function(e){for(var t=1;t<=6;t++){if(1<this.findOrFilter(e,"h"+t).length)return t}return 1},getHeadings:function(e,t){var n="h"+t,r="h"+(t+1);return this.findOrFilter(e,n+","+r)},getNavLevel:function(e){return parseInt(e.tagName.charAt(1),10)},populateNav:function(r,a,e){var i,s=r,c=this;e.each(function(e,t){var n=c.generateNavItem(t);c.getNavLevel(t)===a?s=r:i&&s===r&&(s=c.createChildNavList(i)),s.append(n),i=n})},parseOps:function(e){var t;return(t=e.jquery?{$nav:e}:e).$scope=t.$scope||a(document.body),t}},init:function(e){(e=this.helpers.parseOps(e)).$nav.attr("data-toggle","toc");var t=this.helpers.createChildNavList(e.$nav),n=this.helpers.getTopLevel(e.$scope),r=this.helpers.getHeadings(e.$scope,n);this.helpers.populateNav(t,n,r)}},a(function(){a('nav[data-toggle="toc"]').each(function(e,t){var n=a(t);Toc.init(n)})})}(jQuery);
\ No newline at end of file
diff --git a/deps/clipboard.js-2.0.11/clipboard.min.js b/deps/clipboard.js-2.0.11/clipboard.min.js
new file mode 100644
index 0000000..1103f81
--- /dev/null
+++ b/deps/clipboard.js-2.0.11/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.11
+ * https://clipboardjs.com/
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body},n="";return"string"==typeof t?n=o(t,e):t instanceof HTMLInputElement&&!["text","search","url","tel","password"].includes(null==t?void 0:t.type)?n=o(t.value,e):(n=r()(t),c("copy")),n};function l(t){return(l="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var s=function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{},e=t.action,n=void 0===e?"copy":e,o=t.container,e=t.target,t=t.text;if("copy"!==n&&"cut"!==n)throw new Error('Invalid "action" value, use either "copy" or "cut"');if(void 0!==e){if(!e||"object"!==l(e)||1!==e.nodeType)throw new Error('Invalid "target" value, use a valid Element');if("copy"===n&&e.hasAttribute("disabled"))throw new Error('Invalid "target" attribute. 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t=o?(t=v(this).constructor,Reflect.construct(e,arguments,t)):e.apply(this,arguments),e=this,!(t=t)||"object"!==p(t)&&"function"!=typeof t?function(t){if(void 0!==t)return t;throw new ReferenceError("this hasn't been initialised - super() hasn't been called")}(e):t}}function v(t){return(v=Object.setPrototypeOf?Object.getPrototypeOf:function(t){return t.__proto__||Object.getPrototypeOf(t)})(t)}function m(t,e){t="data-clipboard-".concat(t);if(e.hasAttribute(t))return e.getAttribute(t)}var b=function(){!function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Super expression must either be null or a function");t.prototype=Object.create(e&&e.prototype,{constructor:{value:t,writable:!0,configurable:!0}}),e&&y(t,e)}(r,i());var t,e,n,o=h(r);function r(t,e){var n;return function(t){if(!(t instanceof r))throw new TypeError("Cannot call a class as a function")}(this),(n=o.call(this)).resolveOptions(e),n.listenClick(t),n}return t=r,n=[{key:"copy",value:function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body};return f(t,e)}},{key:"cut",value:function(t){return a(t)}},{key:"isSupported",value:function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:["copy","cut"],t="string"==typeof t?[t]:t,e=!!document.queryCommandSupported;return t.forEach(function(t){e=e&&!!document.queryCommandSupported(t)}),e}}],(e=[{key:"resolveOptions",value:function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{};this.action="function"==typeof t.action?t.action:this.defaultAction,this.target="function"==typeof t.target?t.target:this.defaultTarget,this.text="function"==typeof t.text?t.text:this.defaultText,this.container="object"===p(t.container)?t.container:document.body}},{key:"listenClick",value:function(t){var e=this;this.listener=u()(t,"click",function(t){return e.onClick(t)})}},{key:"onClick",value:function(t){var e=t.delegateTarget||t.currentTarget,n=this.action(e)||"copy",t=s({action:n,container:this.container,target:this.target(e),text:this.text(e)});this.emit(t?"success":"error",{action:n,text:t,trigger:e,clearSelection:function(){e&&e.focus(),window.getSelection().removeAllRanges()}})}},{key:"defaultAction",value:function(t){return m("action",t)}},{key:"defaultTarget",value:function(t){t=m("target",t);if(t)return document.querySelector(t)}},{key:"defaultText",value:function(t){return m("text",t)}},{key:"destroy",value:function(){this.listener.destroy()}}])&&d(t.prototype,e),n&&d(t,n),r}()},828:function(t){var e;"undefined"==typeof Element||Element.prototype.matches||((e=Element.prototype).matches=e.matchesSelector||e.mozMatchesSelector||e.msMatchesSelector||e.oMatchesSelector||e.webkitMatchesSelector),t.exports=function(t,e){for(;t&&9!==t.nodeType;){if("function"==typeof t.matches&&t.matches(e))return t;t=t.parentNode}}},438:function(t,e,n){var u=n(828);function i(t,e,n,o,r){var 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e,n="SELECT"===t.nodeName?(t.focus(),t.value):"INPUT"===t.nodeName||"TEXTAREA"===t.nodeName?((e=t.hasAttribute("readonly"))||t.setAttribute("readonly",""),t.select(),t.setSelectionRange(0,t.value.length),e||t.removeAttribute("readonly"),t.value):(t.hasAttribute("contenteditable")&&t.focus(),n=window.getSelection(),(e=document.createRange()).selectNodeContents(t),n.removeAllRanges(),n.addRange(e),n.toString());return n}},279:function(t){function e(){}e.prototype={on:function(t,e,n){var o=this.e||(this.e={});return(o[t]||(o[t]=[])).push({fn:e,ctx:n}),this},once:function(t,e,n){var o=this;function r(){o.off(t,r),e.apply(n,arguments)}return r._=e,this.on(t,r,n)},emit:function(t){for(var e=[].slice.call(arguments,1),n=((this.e||(this.e={}))[t]||[]).slice(),o=0,r=n.length;o<r;o++)n[o].fn.apply(n[o].ctx,e);return this},off:function(t,e){var n=this.e||(this.e={}),o=n[t],r=[];if(o&&e)for(var i=0,u=o.length;i<u;i++)o[i].fn!==e&&o[i].fn._!==e&&r.push(o[i]);return r.length?n[t]=r:delete 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\ No newline at end of file
diff --git a/deps/data-deps.txt b/deps/data-deps.txt
index 693b82d..8aa49e2 100644
--- a/deps/data-deps.txt
+++ b/deps/data-deps.txt
@@ -2,3 +2,12 @@
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet" />
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script>
+<link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
+<script src="deps/headroom-0.11.0/headroom.min.js"></script>
+<script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script>
+<script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script>
+<script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script>
+<script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script>
+<script src="deps/search-1.0.0/fuse.min.js"></script>
+<script src="deps/search-1.0.0/mark.min.js"></script>
diff --git a/deps/font-awesome-6.4.2/css/all.css b/deps/font-awesome-6.4.2/css/all.css
new file mode 100644
index 0000000..bdb6e3a
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/all.css
@@ -0,0 +1,7968 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa {
+  font-family: var(--fa-style-family, "Font Awesome 6 Free");
+  font-weight: var(--fa-style, 900); }
+
+.fa,
+.fa-classic,
+.fa-sharp,
+.fas,
+.fa-solid,
+.far,
+.fa-regular,
+.fab,
+.fa-brands {
+  -moz-osx-font-smoothing: grayscale;
+  -webkit-font-smoothing: antialiased;
+  display: var(--fa-display, inline-block);
+  font-style: normal;
+  font-variant: normal;
+  line-height: 1;
+  text-rendering: auto; }
+
+.fas,
+.fa-classic,
+.fa-solid,
+.far,
+.fa-regular {
+  font-family: 'Font Awesome 6 Free'; }
+
+.fab,
+.fa-brands {
+  font-family: 'Font Awesome 6 Brands'; }
+
+.fa-1x {
+  font-size: 1em; }
+
+.fa-2x {
+  font-size: 2em; }
+
+.fa-3x {
+  font-size: 3em; }
+
+.fa-4x {
+  font-size: 4em; }
+
+.fa-5x {
+  font-size: 5em; }
+
+.fa-6x {
+  font-size: 6em; }
+
+.fa-7x {
+  font-size: 7em; }
+
+.fa-8x {
+  font-size: 8em; }
+
+.fa-9x {
+  font-size: 9em; }
+
+.fa-10x {
+  font-size: 10em; }
+
+.fa-2xs {
+  font-size: 0.625em;
+  line-height: 0.1em;
+  vertical-align: 0.225em; }
+
+.fa-xs {
+  font-size: 0.75em;
+  line-height: 0.08333em;
+  vertical-align: 0.125em; }
+
+.fa-sm {
+  font-size: 0.875em;
+  line-height: 0.07143em;
+  vertical-align: 0.05357em; }
+
+.fa-lg {
+  font-size: 1.25em;
+  line-height: 0.05em;
+  vertical-align: -0.075em; }
+
+.fa-xl {
+  font-size: 1.5em;
+  line-height: 0.04167em;
+  vertical-align: -0.125em; }
+
+.fa-2xl {
+  font-size: 2em;
+  line-height: 0.03125em;
+  vertical-align: -0.1875em; }
+
+.fa-fw {
+  text-align: center;
+  width: 1.25em; }
+
+.fa-ul {
+  list-style-type: none;
+  margin-left: var(--fa-li-margin, 2.5em);
+  padding-left: 0; }
+  .fa-ul > li {
+    position: relative; }
+
+.fa-li {
+  left: calc(var(--fa-li-width, 2em) * -1);
+  position: absolute;
+  text-align: center;
+  width: var(--fa-li-width, 2em);
+  line-height: inherit; }
+
+.fa-border {
+  border-color: var(--fa-border-color, #eee);
+  border-radius: var(--fa-border-radius, 0.1em);
+  border-style: var(--fa-border-style, solid);
+  border-width: var(--fa-border-width, 0.08em);
+  padding: var(--fa-border-padding, 0.2em 0.25em 0.15em); }
+
+.fa-pull-left {
+  float: left;
+  margin-right: var(--fa-pull-margin, 0.3em); }
+
+.fa-pull-right {
+  float: right;
+  margin-left: var(--fa-pull-margin, 0.3em); }
+
+.fa-beat {
+  -webkit-animation-name: fa-beat;
+          animation-name: fa-beat;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-bounce {
+  -webkit-animation-name: fa-bounce;
+          animation-name: fa-bounce;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.28, 0.84, 0.42, 1)); }
+
+.fa-fade {
+  -webkit-animation-name: fa-fade;
+          animation-name: fa-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-beat-fade {
+  -webkit-animation-name: fa-beat-fade;
+          animation-name: fa-beat-fade;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1));
+          animation-timing-function: var(--fa-animation-timing, cubic-bezier(0.4, 0, 0.6, 1)); }
+
+.fa-flip {
+  -webkit-animation-name: fa-flip;
+          animation-name: fa-flip;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, ease-in-out);
+          animation-timing-function: var(--fa-animation-timing, ease-in-out); }
+
+.fa-shake {
+  -webkit-animation-name: fa-shake;
+          animation-name: fa-shake;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-delay: var(--fa-animation-delay, 0s);
+          animation-delay: var(--fa-animation-delay, 0s);
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 2s);
+          animation-duration: var(--fa-animation-duration, 2s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, linear);
+          animation-timing-function: var(--fa-animation-timing, linear); }
+
+.fa-spin-reverse {
+  --fa-animation-direction: reverse; }
+
+.fa-pulse,
+.fa-spin-pulse {
+  -webkit-animation-name: fa-spin;
+          animation-name: fa-spin;
+  -webkit-animation-direction: var(--fa-animation-direction, normal);
+          animation-direction: var(--fa-animation-direction, normal);
+  -webkit-animation-duration: var(--fa-animation-duration, 1s);
+          animation-duration: var(--fa-animation-duration, 1s);
+  -webkit-animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+          animation-iteration-count: var(--fa-animation-iteration-count, infinite);
+  -webkit-animation-timing-function: var(--fa-animation-timing, steps(8));
+          animation-timing-function: var(--fa-animation-timing, steps(8)); }
+
+@media (prefers-reduced-motion: reduce) {
+  .fa-beat,
+  .fa-bounce,
+  .fa-fade,
+  .fa-beat-fade,
+  .fa-flip,
+  .fa-pulse,
+  .fa-shake,
+  .fa-spin,
+  .fa-spin-pulse {
+    -webkit-animation-delay: -1ms;
+            animation-delay: -1ms;
+    -webkit-animation-duration: 1ms;
+            animation-duration: 1ms;
+    -webkit-animation-iteration-count: 1;
+            animation-iteration-count: 1;
+    -webkit-transition-delay: 0s;
+            transition-delay: 0s;
+    -webkit-transition-duration: 0s;
+            transition-duration: 0s; } }
+
+@-webkit-keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@keyframes fa-beat {
+  0%, 90% {
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  45% {
+    -webkit-transform: scale(var(--fa-beat-scale, 1.25));
+            transform: scale(var(--fa-beat-scale, 1.25)); } }
+
+@-webkit-keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@keyframes fa-bounce {
+  0% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  10% {
+    -webkit-transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0);
+            transform: scale(var(--fa-bounce-start-scale-x, 1.1), var(--fa-bounce-start-scale-y, 0.9)) translateY(0); }
+  30% {
+    -webkit-transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em));
+            transform: scale(var(--fa-bounce-jump-scale-x, 0.9), var(--fa-bounce-jump-scale-y, 1.1)) translateY(var(--fa-bounce-height, -0.5em)); }
+  50% {
+    -webkit-transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0);
+            transform: scale(var(--fa-bounce-land-scale-x, 1.05), var(--fa-bounce-land-scale-y, 0.95)) translateY(0); }
+  57% {
+    -webkit-transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em));
+            transform: scale(1, 1) translateY(var(--fa-bounce-rebound, -0.125em)); }
+  64% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); }
+  100% {
+    -webkit-transform: scale(1, 1) translateY(0);
+            transform: scale(1, 1) translateY(0); } }
+
+@-webkit-keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@keyframes fa-fade {
+  50% {
+    opacity: var(--fa-fade-opacity, 0.4); } }
+
+@-webkit-keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@keyframes fa-beat-fade {
+  0%, 100% {
+    opacity: var(--fa-beat-fade-opacity, 0.4);
+    -webkit-transform: scale(1);
+            transform: scale(1); }
+  50% {
+    opacity: 1;
+    -webkit-transform: scale(var(--fa-beat-fade-scale, 1.125));
+            transform: scale(var(--fa-beat-fade-scale, 1.125)); } }
+
+@-webkit-keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@keyframes fa-flip {
+  50% {
+    -webkit-transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg));
+            transform: rotate3d(var(--fa-flip-x, 0), var(--fa-flip-y, 1), var(--fa-flip-z, 0), var(--fa-flip-angle, -180deg)); } }
+
+@-webkit-keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@keyframes fa-shake {
+  0% {
+    -webkit-transform: rotate(-15deg);
+            transform: rotate(-15deg); }
+  4% {
+    -webkit-transform: rotate(15deg);
+            transform: rotate(15deg); }
+  8%, 24% {
+    -webkit-transform: rotate(-18deg);
+            transform: rotate(-18deg); }
+  12%, 28% {
+    -webkit-transform: rotate(18deg);
+            transform: rotate(18deg); }
+  16% {
+    -webkit-transform: rotate(-22deg);
+            transform: rotate(-22deg); }
+  20% {
+    -webkit-transform: rotate(22deg);
+            transform: rotate(22deg); }
+  32% {
+    -webkit-transform: rotate(-12deg);
+            transform: rotate(-12deg); }
+  36% {
+    -webkit-transform: rotate(12deg);
+            transform: rotate(12deg); }
+  40%, 100% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); } }
+
+@-webkit-keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+@keyframes fa-spin {
+  0% {
+    -webkit-transform: rotate(0deg);
+            transform: rotate(0deg); }
+  100% {
+    -webkit-transform: rotate(360deg);
+            transform: rotate(360deg); } }
+
+.fa-rotate-90 {
+  -webkit-transform: rotate(90deg);
+          transform: rotate(90deg); }
+
+.fa-rotate-180 {
+  -webkit-transform: rotate(180deg);
+          transform: rotate(180deg); }
+
+.fa-rotate-270 {
+  -webkit-transform: rotate(270deg);
+          transform: rotate(270deg); }
+
+.fa-flip-horizontal {
+  -webkit-transform: scale(-1, 1);
+          transform: scale(-1, 1); }
+
+.fa-flip-vertical {
+  -webkit-transform: scale(1, -1);
+          transform: scale(1, -1); }
+
+.fa-flip-both,
+.fa-flip-horizontal.fa-flip-vertical {
+  -webkit-transform: scale(-1, -1);
+          transform: scale(-1, -1); }
+
+.fa-rotate-by {
+  -webkit-transform: rotate(var(--fa-rotate-angle, none));
+          transform: rotate(var(--fa-rotate-angle, none)); }
+
+.fa-stack {
+  display: inline-block;
+  height: 2em;
+  line-height: 2em;
+  position: relative;
+  vertical-align: middle;
+  width: 2.5em; }
+
+.fa-stack-1x,
+.fa-stack-2x {
+  left: 0;
+  position: absolute;
+  text-align: center;
+  width: 100%;
+  z-index: var(--fa-stack-z-index, auto); }
+
+.fa-stack-1x {
+  line-height: inherit; }
+
+.fa-stack-2x {
+  font-size: 2em; }
+
+.fa-inverse {
+  color: var(--fa-inverse, #fff); }
+
+/* Font Awesome uses the Unicode Private Use Area (PUA) to ensure screen
+readers do not read off random characters that represent icons */
+
+.fa-0::before {
+  content: "\30"; }
+
+.fa-1::before {
+  content: "\31"; }
+
+.fa-2::before {
+  content: "\32"; }
+
+.fa-3::before {
+  content: "\33"; }
+
+.fa-4::before {
+  content: "\34"; }
+
+.fa-5::before {
+  content: "\35"; }
+
+.fa-6::before {
+  content: "\36"; }
+
+.fa-7::before {
+  content: "\37"; }
+
+.fa-8::before {
+  content: "\38"; }
+
+.fa-9::before {
+  content: "\39"; }
+
+.fa-fill-drip::before {
+  content: "\f576"; }
+
+.fa-arrows-to-circle::before {
+  content: "\e4bd"; }
+
+.fa-circle-chevron-right::before {
+  content: "\f138"; }
+
+.fa-chevron-circle-right::before {
+  content: "\f138"; }
+
+.fa-at::before {
+  content: "\40"; }
+
+.fa-trash-can::before {
+  content: "\f2ed"; }
+
+.fa-trash-alt::before {
+  content: "\f2ed"; }
+
+.fa-text-height::before {
+  content: "\f034"; }
+
+.fa-user-xmark::before {
+  content: "\f235"; }
+
+.fa-user-times::before {
+  content: "\f235"; }
+
+.fa-stethoscope::before {
+  content: "\f0f1"; }
+
+.fa-message::before {
+  content: "\f27a"; }
+
+.fa-comment-alt::before {
+  content: "\f27a"; }
+
+.fa-info::before {
+  content: "\f129"; }
+
+.fa-down-left-and-up-right-to-center::before {
+  content: "\f422"; }
+
+.fa-compress-alt::before {
+  content: "\f422"; }
+
+.fa-explosion::before {
+  content: "\e4e9"; }
+
+.fa-file-lines::before {
+  content: "\f15c"; }
+
+.fa-file-alt::before {
+  content: "\f15c"; }
+
+.fa-file-text::before {
+  content: "\f15c"; }
+
+.fa-wave-square::before {
+  content: "\f83e"; }
+
+.fa-ring::before {
+  content: "\f70b"; }
+
+.fa-building-un::before {
+  content: "\e4d9"; }
+
+.fa-dice-three::before {
+  content: "\f527"; }
+
+.fa-calendar-days::before {
+  content: "\f073"; }
+
+.fa-calendar-alt::before {
+  content: "\f073"; }
+
+.fa-anchor-circle-check::before {
+  content: "\e4aa"; }
+
+.fa-building-circle-arrow-right::before {
+  content: "\e4d1"; }
+
+.fa-volleyball::before {
+  content: "\f45f"; }
+
+.fa-volleyball-ball::before {
+  content: "\f45f"; }
+
+.fa-arrows-up-to-line::before {
+  content: "\e4c2"; }
+
+.fa-sort-down::before {
+  content: "\f0dd"; }
+
+.fa-sort-desc::before {
+  content: "\f0dd"; }
+
+.fa-circle-minus::before {
+  content: "\f056"; }
+
+.fa-minus-circle::before {
+  content: "\f056"; }
+
+.fa-door-open::before {
+  content: "\f52b"; }
+
+.fa-right-from-bracket::before {
+  content: "\f2f5"; }
+
+.fa-sign-out-alt::before {
+  content: "\f2f5"; }
+
+.fa-atom::before {
+  content: "\f5d2"; }
+
+.fa-soap::before {
+  content: "\e06e"; }
+
+.fa-icons::before {
+  content: "\f86d"; }
+
+.fa-heart-music-camera-bolt::before {
+  content: "\f86d"; }
+
+.fa-microphone-lines-slash::before {
+  content: "\f539"; }
+
+.fa-microphone-alt-slash::before {
+  content: "\f539"; }
+
+.fa-bridge-circle-check::before {
+  content: "\e4c9"; }
+
+.fa-pump-medical::before {
+  content: "\e06a"; }
+
+.fa-fingerprint::before {
+  content: "\f577"; }
+
+.fa-hand-point-right::before {
+  content: "\f0a4"; }
+
+.fa-magnifying-glass-location::before {
+  content: "\f689"; }
+
+.fa-search-location::before {
+  content: "\f689"; }
+
+.fa-forward-step::before {
+  content: "\f051"; }
+
+.fa-step-forward::before {
+  content: "\f051"; }
+
+.fa-face-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-smile-beam::before {
+  content: "\f5b8"; }
+
+.fa-flag-checkered::before {
+  content: "\f11e"; }
+
+.fa-football::before {
+  content: "\f44e"; }
+
+.fa-football-ball::before {
+  content: "\f44e"; }
+
+.fa-school-circle-exclamation::before {
+  content: "\e56c"; }
+
+.fa-crop::before {
+  content: "\f125"; }
+
+.fa-angles-down::before {
+  content: "\f103"; }
+
+.fa-angle-double-down::before {
+  content: "\f103"; }
+
+.fa-users-rectangle::before {
+  content: "\e594"; }
+
+.fa-people-roof::before {
+  content: "\e537"; }
+
+.fa-people-line::before {
+  content: "\e534"; }
+
+.fa-beer-mug-empty::before {
+  content: "\f0fc"; }
+
+.fa-beer::before {
+  content: "\f0fc"; }
+
+.fa-diagram-predecessor::before {
+  content: "\e477"; }
+
+.fa-arrow-up-long::before {
+  content: "\f176"; }
+
+.fa-long-arrow-up::before {
+  content: "\f176"; }
+
+.fa-fire-flame-simple::before {
+  content: "\f46a"; }
+
+.fa-burn::before {
+  content: "\f46a"; }
+
+.fa-person::before {
+  content: "\f183"; }
+
+.fa-male::before {
+  content: "\f183"; }
+
+.fa-laptop::before {
+  content: "\f109"; }
+
+.fa-file-csv::before {
+  content: "\f6dd"; }
+
+.fa-menorah::before {
+  content: "\f676"; }
+
+.fa-truck-plane::before {
+  content: "\e58f"; }
+
+.fa-record-vinyl::before {
+  content: "\f8d9"; }
+
+.fa-face-grin-stars::before {
+  content: "\f587"; }
+
+.fa-grin-stars::before {
+  content: "\f587"; }
+
+.fa-bong::before {
+  content: "\f55c"; }
+
+.fa-spaghetti-monster-flying::before {
+  content: "\f67b"; }
+
+.fa-pastafarianism::before {
+  content: "\f67b"; }
+
+.fa-arrow-down-up-across-line::before {
+  content: "\e4af"; }
+
+.fa-spoon::before {
+  content: "\f2e5"; }
+
+.fa-utensil-spoon::before {
+  content: "\f2e5"; }
+
+.fa-jar-wheat::before {
+  content: "\e517"; }
+
+.fa-envelopes-bulk::before {
+  content: "\f674"; }
+
+.fa-mail-bulk::before {
+  content: "\f674"; }
+
+.fa-file-circle-exclamation::before {
+  content: "\e4eb"; }
+
+.fa-circle-h::before {
+  content: "\f47e"; }
+
+.fa-hospital-symbol::before {
+  content: "\f47e"; }
+
+.fa-pager::before {
+  content: "\f815"; }
+
+.fa-address-book::before {
+  content: "\f2b9"; }
+
+.fa-contact-book::before {
+  content: "\f2b9"; }
+
+.fa-strikethrough::before {
+  content: "\f0cc"; }
+
+.fa-k::before {
+  content: "\4b"; }
+
+.fa-landmark-flag::before {
+  content: "\e51c"; }
+
+.fa-pencil::before {
+  content: "\f303"; }
+
+.fa-pencil-alt::before {
+  content: "\f303"; }
+
+.fa-backward::before {
+  content: "\f04a"; }
+
+.fa-caret-right::before {
+  content: "\f0da"; }
+
+.fa-comments::before {
+  content: "\f086"; }
+
+.fa-paste::before {
+  content: "\f0ea"; }
+
+.fa-file-clipboard::before {
+  content: "\f0ea"; }
+
+.fa-code-pull-request::before {
+  content: "\e13c"; }
+
+.fa-clipboard-list::before {
+  content: "\f46d"; }
+
+.fa-truck-ramp-box::before {
+  content: "\f4de"; }
+
+.fa-truck-loading::before {
+  content: "\f4de"; }
+
+.fa-user-check::before {
+  content: "\f4fc"; }
+
+.fa-vial-virus::before {
+  content: "\e597"; }
+
+.fa-sheet-plastic::before {
+  content: "\e571"; }
+
+.fa-blog::before {
+  content: "\f781"; }
+
+.fa-user-ninja::before {
+  content: "\f504"; }
+
+.fa-person-arrow-up-from-line::before {
+  content: "\e539"; }
+
+.fa-scroll-torah::before {
+  content: "\f6a0"; }
+
+.fa-torah::before {
+  content: "\f6a0"; }
+
+.fa-broom-ball::before {
+  content: "\f458"; }
+
+.fa-quidditch::before {
+  content: "\f458"; }
+
+.fa-quidditch-broom-ball::before {
+  content: "\f458"; }
+
+.fa-toggle-off::before {
+  content: "\f204"; }
+
+.fa-box-archive::before {
+  content: "\f187"; }
+
+.fa-archive::before {
+  content: "\f187"; }
+
+.fa-person-drowning::before {
+  content: "\e545"; }
+
+.fa-arrow-down-9-1::before {
+  content: "\f886"; }
+
+.fa-sort-numeric-desc::before {
+  content: "\f886"; }
+
+.fa-sort-numeric-down-alt::before {
+  content: "\f886"; }
+
+.fa-face-grin-tongue-squint::before {
+  content: "\f58a"; }
+
+.fa-grin-tongue-squint::before {
+  content: "\f58a"; }
+
+.fa-spray-can::before {
+  content: "\f5bd"; }
+
+.fa-truck-monster::before {
+  content: "\f63b"; }
+
+.fa-w::before {
+  content: "\57"; }
+
+.fa-earth-africa::before {
+  content: "\f57c"; }
+
+.fa-globe-africa::before {
+  content: "\f57c"; }
+
+.fa-rainbow::before {
+  content: "\f75b"; }
+
+.fa-circle-notch::before {
+  content: "\f1ce"; }
+
+.fa-tablet-screen-button::before {
+  content: "\f3fa"; }
+
+.fa-tablet-alt::before {
+  content: "\f3fa"; }
+
+.fa-paw::before {
+  content: "\f1b0"; }
+
+.fa-cloud::before {
+  content: "\f0c2"; }
+
+.fa-trowel-bricks::before {
+  content: "\e58a"; }
+
+.fa-face-flushed::before {
+  content: "\f579"; }
+
+.fa-flushed::before {
+  content: "\f579"; }
+
+.fa-hospital-user::before {
+  content: "\f80d"; }
+
+.fa-tent-arrow-left-right::before {
+  content: "\e57f"; }
+
+.fa-gavel::before {
+  content: "\f0e3"; }
+
+.fa-legal::before {
+  content: "\f0e3"; }
+
+.fa-binoculars::before {
+  content: "\f1e5"; }
+
+.fa-microphone-slash::before {
+  content: "\f131"; }
+
+.fa-box-tissue::before {
+  content: "\e05b"; }
+
+.fa-motorcycle::before {
+  content: "\f21c"; }
+
+.fa-bell-concierge::before {
+  content: "\f562"; }
+
+.fa-concierge-bell::before {
+  content: "\f562"; }
+
+.fa-pen-ruler::before {
+  content: "\f5ae"; }
+
+.fa-pencil-ruler::before {
+  content: "\f5ae"; }
+
+.fa-people-arrows::before {
+  content: "\e068"; }
+
+.fa-people-arrows-left-right::before {
+  content: "\e068"; }
+
+.fa-mars-and-venus-burst::before {
+  content: "\e523"; }
+
+.fa-square-caret-right::before {
+  content: "\f152"; }
+
+.fa-caret-square-right::before {
+  content: "\f152"; }
+
+.fa-scissors::before {
+  content: "\f0c4"; }
+
+.fa-cut::before {
+  content: "\f0c4"; }
+
+.fa-sun-plant-wilt::before {
+  content: "\e57a"; }
+
+.fa-toilets-portable::before {
+  content: "\e584"; }
+
+.fa-hockey-puck::before {
+  content: "\f453"; }
+
+.fa-table::before {
+  content: "\f0ce"; }
+
+.fa-magnifying-glass-arrow-right::before {
+  content: "\e521"; }
+
+.fa-tachograph-digital::before {
+  content: "\f566"; }
+
+.fa-digital-tachograph::before {
+  content: "\f566"; }
+
+.fa-users-slash::before {
+  content: "\e073"; }
+
+.fa-clover::before {
+  content: "\e139"; }
+
+.fa-reply::before {
+  content: "\f3e5"; }
+
+.fa-mail-reply::before {
+  content: "\f3e5"; }
+
+.fa-star-and-crescent::before {
+  content: "\f699"; }
+
+.fa-house-fire::before {
+  content: "\e50c"; }
+
+.fa-square-minus::before {
+  content: "\f146"; }
+
+.fa-minus-square::before {
+  content: "\f146"; }
+
+.fa-helicopter::before {
+  content: "\f533"; }
+
+.fa-compass::before {
+  content: "\f14e"; }
+
+.fa-square-caret-down::before {
+  content: "\f150"; }
+
+.fa-caret-square-down::before {
+  content: "\f150"; }
+
+.fa-file-circle-question::before {
+  content: "\e4ef"; }
+
+.fa-laptop-code::before {
+  content: "\f5fc"; }
+
+.fa-swatchbook::before {
+  content: "\f5c3"; }
+
+.fa-prescription-bottle::before {
+  content: "\f485"; }
+
+.fa-bars::before {
+  content: "\f0c9"; }
+
+.fa-navicon::before {
+  content: "\f0c9"; }
+
+.fa-people-group::before {
+  content: "\e533"; }
+
+.fa-hourglass-end::before {
+  content: "\f253"; }
+
+.fa-hourglass-3::before {
+  content: "\f253"; }
+
+.fa-heart-crack::before {
+  content: "\f7a9"; }
+
+.fa-heart-broken::before {
+  content: "\f7a9"; }
+
+.fa-square-up-right::before {
+  content: "\f360"; }
+
+.fa-external-link-square-alt::before {
+  content: "\f360"; }
+
+.fa-face-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-kiss-beam::before {
+  content: "\f597"; }
+
+.fa-film::before {
+  content: "\f008"; }
+
+.fa-ruler-horizontal::before {
+  content: "\f547"; }
+
+.fa-people-robbery::before {
+  content: "\e536"; }
+
+.fa-lightbulb::before {
+  content: "\f0eb"; }
+
+.fa-caret-left::before {
+  content: "\f0d9"; }
+
+.fa-circle-exclamation::before {
+  content: "\f06a"; }
+
+.fa-exclamation-circle::before {
+  content: "\f06a"; }
+
+.fa-school-circle-xmark::before {
+  content: "\e56d"; }
+
+.fa-arrow-right-from-bracket::before {
+  content: "\f08b"; }
+
+.fa-sign-out::before {
+  content: "\f08b"; }
+
+.fa-circle-chevron-down::before {
+  content: "\f13a"; }
+
+.fa-chevron-circle-down::before {
+  content: "\f13a"; }
+
+.fa-unlock-keyhole::before {
+  content: "\f13e"; }
+
+.fa-unlock-alt::before {
+  content: "\f13e"; }
+
+.fa-cloud-showers-heavy::before {
+  content: "\f740"; }
+
+.fa-headphones-simple::before {
+  content: "\f58f"; }
+
+.fa-headphones-alt::before {
+  content: "\f58f"; }
+
+.fa-sitemap::before {
+  content: "\f0e8"; }
+
+.fa-circle-dollar-to-slot::before {
+  content: "\f4b9"; }
+
+.fa-donate::before {
+  content: "\f4b9"; }
+
+.fa-memory::before {
+  content: "\f538"; }
+
+.fa-road-spikes::before {
+  content: "\e568"; }
+
+.fa-fire-burner::before {
+  content: "\e4f1"; }
+
+.fa-flag::before {
+  content: "\f024"; }
+
+.fa-hanukiah::before {
+  content: "\f6e6"; }
+
+.fa-feather::before {
+  content: "\f52d"; }
+
+.fa-volume-low::before {
+  content: "\f027"; }
+
+.fa-volume-down::before {
+  content: "\f027"; }
+
+.fa-comment-slash::before {
+  content: "\f4b3"; }
+
+.fa-cloud-sun-rain::before {
+  content: "\f743"; }
+
+.fa-compress::before {
+  content: "\f066"; }
+
+.fa-wheat-awn::before {
+  content: "\e2cd"; }
+
+.fa-wheat-alt::before {
+  content: "\e2cd"; }
+
+.fa-ankh::before {
+  content: "\f644"; }
+
+.fa-hands-holding-child::before {
+  content: "\e4fa"; }
+
+.fa-asterisk::before {
+  content: "\2a"; }
+
+.fa-square-check::before {
+  content: "\f14a"; }
+
+.fa-check-square::before {
+  content: "\f14a"; }
+
+.fa-peseta-sign::before {
+  content: "\e221"; }
+
+.fa-heading::before {
+  content: "\f1dc"; }
+
+.fa-header::before {
+  content: "\f1dc"; }
+
+.fa-ghost::before {
+  content: "\f6e2"; }
+
+.fa-list::before {
+  content: "\f03a"; }
+
+.fa-list-squares::before {
+  content: "\f03a"; }
+
+.fa-square-phone-flip::before {
+  content: "\f87b"; }
+
+.fa-phone-square-alt::before {
+  content: "\f87b"; }
+
+.fa-cart-plus::before {
+  content: "\f217"; }
+
+.fa-gamepad::before {
+  content: "\f11b"; }
+
+.fa-circle-dot::before {
+  content: "\f192"; }
+
+.fa-dot-circle::before {
+  content: "\f192"; }
+
+.fa-face-dizzy::before {
+  content: "\f567"; }
+
+.fa-dizzy::before {
+  content: "\f567"; }
+
+.fa-egg::before {
+  content: "\f7fb"; }
+
+.fa-house-medical-circle-xmark::before {
+  content: "\e513"; }
+
+.fa-campground::before {
+  content: "\f6bb"; }
+
+.fa-folder-plus::before {
+  content: "\f65e"; }
+
+.fa-futbol::before {
+  content: "\f1e3"; }
+
+.fa-futbol-ball::before {
+  content: "\f1e3"; }
+
+.fa-soccer-ball::before {
+  content: "\f1e3"; }
+
+.fa-paintbrush::before {
+  content: "\f1fc"; }
+
+.fa-paint-brush::before {
+  content: "\f1fc"; }
+
+.fa-lock::before {
+  content: "\f023"; }
+
+.fa-gas-pump::before {
+  content: "\f52f"; }
+
+.fa-hot-tub-person::before {
+  content: "\f593"; }
+
+.fa-hot-tub::before {
+  content: "\f593"; }
+
+.fa-map-location::before {
+  content: "\f59f"; }
+
+.fa-map-marked::before {
+  content: "\f59f"; }
+
+.fa-house-flood-water::before {
+  content: "\e50e"; }
+
+.fa-tree::before {
+  content: "\f1bb"; }
+
+.fa-bridge-lock::before {
+  content: "\e4cc"; }
+
+.fa-sack-dollar::before {
+  content: "\f81d"; }
+
+.fa-pen-to-square::before {
+  content: "\f044"; }
+
+.fa-edit::before {
+  content: "\f044"; }
+
+.fa-car-side::before {
+  content: "\f5e4"; }
+
+.fa-share-nodes::before {
+  content: "\f1e0"; }
+
+.fa-share-alt::before {
+  content: "\f1e0"; }
+
+.fa-heart-circle-minus::before {
+  content: "\e4ff"; }
+
+.fa-hourglass-half::before {
+  content: "\f252"; }
+
+.fa-hourglass-2::before {
+  content: "\f252"; }
+
+.fa-microscope::before {
+  content: "\f610"; }
+
+.fa-sink::before {
+  content: "\e06d"; }
+
+.fa-bag-shopping::before {
+  content: "\f290"; }
+
+.fa-shopping-bag::before {
+  content: "\f290"; }
+
+.fa-arrow-down-z-a::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-desc::before {
+  content: "\f881"; }
+
+.fa-sort-alpha-down-alt::before {
+  content: "\f881"; }
+
+.fa-mitten::before {
+  content: "\f7b5"; }
+
+.fa-person-rays::before {
+  content: "\e54d"; }
+
+.fa-users::before {
+  content: "\f0c0"; }
+
+.fa-eye-slash::before {
+  content: "\f070"; }
+
+.fa-flask-vial::before {
+  content: "\e4f3"; }
+
+.fa-hand::before {
+  content: "\f256"; }
+
+.fa-hand-paper::before {
+  content: "\f256"; }
+
+.fa-om::before {
+  content: "\f679"; }
+
+.fa-worm::before {
+  content: "\e599"; }
+
+.fa-house-circle-xmark::before {
+  content: "\e50b"; }
+
+.fa-plug::before {
+  content: "\f1e6"; }
+
+.fa-chevron-up::before {
+  content: "\f077"; }
+
+.fa-hand-spock::before {
+  content: "\f259"; }
+
+.fa-stopwatch::before {
+  content: "\f2f2"; }
+
+.fa-face-kiss::before {
+  content: "\f596"; }
+
+.fa-kiss::before {
+  content: "\f596"; }
+
+.fa-bridge-circle-xmark::before {
+  content: "\e4cb"; }
+
+.fa-face-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-grin-tongue::before {
+  content: "\f589"; }
+
+.fa-chess-bishop::before {
+  content: "\f43a"; }
+
+.fa-face-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-grin-wink::before {
+  content: "\f58c"; }
+
+.fa-ear-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deaf::before {
+  content: "\f2a4"; }
+
+.fa-deafness::before {
+  content: "\f2a4"; }
+
+.fa-hard-of-hearing::before {
+  content: "\f2a4"; }
+
+.fa-road-circle-check::before {
+  content: "\e564"; }
+
+.fa-dice-five::before {
+  content: "\f523"; }
+
+.fa-square-rss::before {
+  content: "\f143"; }
+
+.fa-rss-square::before {
+  content: "\f143"; }
+
+.fa-land-mine-on::before {
+  content: "\e51b"; }
+
+.fa-i-cursor::before {
+  content: "\f246"; }
+
+.fa-stamp::before {
+  content: "\f5bf"; }
+
+.fa-stairs::before {
+  content: "\e289"; }
+
+.fa-i::before {
+  content: "\49"; }
+
+.fa-hryvnia-sign::before {
+  content: "\f6f2"; }
+
+.fa-hryvnia::before {
+  content: "\f6f2"; }
+
+.fa-pills::before {
+  content: "\f484"; }
+
+.fa-face-grin-wide::before {
+  content: "\f581"; }
+
+.fa-grin-alt::before {
+  content: "\f581"; }
+
+.fa-tooth::before {
+  content: "\f5c9"; }
+
+.fa-v::before {
+  content: "\56"; }
+
+.fa-bangladeshi-taka-sign::before {
+  content: "\e2e6"; }
+
+.fa-bicycle::before {
+  content: "\f206"; }
+
+.fa-staff-snake::before {
+  content: "\e579"; }
+
+.fa-rod-asclepius::before {
+  content: "\e579"; }
+
+.fa-rod-snake::before {
+  content: "\e579"; }
+
+.fa-staff-aesculapius::before {
+  content: "\e579"; }
+
+.fa-head-side-cough-slash::before {
+  content: "\e062"; }
+
+.fa-truck-medical::before {
+  content: "\f0f9"; }
+
+.fa-ambulance::before {
+  content: "\f0f9"; }
+
+.fa-wheat-awn-circle-exclamation::before {
+  content: "\e598"; }
+
+.fa-snowman::before {
+  content: "\f7d0"; }
+
+.fa-mortar-pestle::before {
+  content: "\f5a7"; }
+
+.fa-road-barrier::before {
+  content: "\e562"; }
+
+.fa-school::before {
+  content: "\f549"; }
+
+.fa-igloo::before {
+  content: "\f7ae"; }
+
+.fa-joint::before {
+  content: "\f595"; }
+
+.fa-angle-right::before {
+  content: "\f105"; }
+
+.fa-horse::before {
+  content: "\f6f0"; }
+
+.fa-q::before {
+  content: "\51"; }
+
+.fa-g::before {
+  content: "\47"; }
+
+.fa-notes-medical::before {
+  content: "\f481"; }
+
+.fa-temperature-half::before {
+  content: "\f2c9"; }
+
+.fa-temperature-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-2::before {
+  content: "\f2c9"; }
+
+.fa-thermometer-half::before {
+  content: "\f2c9"; }
+
+.fa-dong-sign::before {
+  content: "\e169"; }
+
+.fa-capsules::before {
+  content: "\f46b"; }
+
+.fa-poo-storm::before {
+  content: "\f75a"; }
+
+.fa-poo-bolt::before {
+  content: "\f75a"; }
+
+.fa-face-frown-open::before {
+  content: "\f57a"; }
+
+.fa-frown-open::before {
+  content: "\f57a"; }
+
+.fa-hand-point-up::before {
+  content: "\f0a6"; }
+
+.fa-money-bill::before {
+  content: "\f0d6"; }
+
+.fa-bookmark::before {
+  content: "\f02e"; }
+
+.fa-align-justify::before {
+  content: "\f039"; }
+
+.fa-umbrella-beach::before {
+  content: "\f5ca"; }
+
+.fa-helmet-un::before {
+  content: "\e503"; }
+
+.fa-bullseye::before {
+  content: "\f140"; }
+
+.fa-bacon::before {
+  content: "\f7e5"; }
+
+.fa-hand-point-down::before {
+  content: "\f0a7"; }
+
+.fa-arrow-up-from-bracket::before {
+  content: "\e09a"; }
+
+.fa-folder::before {
+  content: "\f07b"; }
+
+.fa-folder-blank::before {
+  content: "\f07b"; }
+
+.fa-file-waveform::before {
+  content: "\f478"; }
+
+.fa-file-medical-alt::before {
+  content: "\f478"; }
+
+.fa-radiation::before {
+  content: "\f7b9"; }
+
+.fa-chart-simple::before {
+  content: "\e473"; }
+
+.fa-mars-stroke::before {
+  content: "\f229"; }
+
+.fa-vial::before {
+  content: "\f492"; }
+
+.fa-gauge::before {
+  content: "\f624"; }
+
+.fa-dashboard::before {
+  content: "\f624"; }
+
+.fa-gauge-med::before {
+  content: "\f624"; }
+
+.fa-tachometer-alt-average::before {
+  content: "\f624"; }
+
+.fa-wand-magic-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-magic-wand-sparkles::before {
+  content: "\e2ca"; }
+
+.fa-e::before {
+  content: "\45"; }
+
+.fa-pen-clip::before {
+  content: "\f305"; }
+
+.fa-pen-alt::before {
+  content: "\f305"; }
+
+.fa-bridge-circle-exclamation::before {
+  content: "\e4ca"; }
+
+.fa-user::before {
+  content: "\f007"; }
+
+.fa-school-circle-check::before {
+  content: "\e56b"; }
+
+.fa-dumpster::before {
+  content: "\f793"; }
+
+.fa-van-shuttle::before {
+  content: "\f5b6"; }
+
+.fa-shuttle-van::before {
+  content: "\f5b6"; }
+
+.fa-building-user::before {
+  content: "\e4da"; }
+
+.fa-square-caret-left::before {
+  content: "\f191"; }
+
+.fa-caret-square-left::before {
+  content: "\f191"; }
+
+.fa-highlighter::before {
+  content: "\f591"; }
+
+.fa-key::before {
+  content: "\f084"; }
+
+.fa-bullhorn::before {
+  content: "\f0a1"; }
+
+.fa-globe::before {
+  content: "\f0ac"; }
+
+.fa-synagogue::before {
+  content: "\f69b"; }
+
+.fa-person-half-dress::before {
+  content: "\e548"; }
+
+.fa-road-bridge::before {
+  content: "\e563"; }
+
+.fa-location-arrow::before {
+  content: "\f124"; }
+
+.fa-c::before {
+  content: "\43"; }
+
+.fa-tablet-button::before {
+  content: "\f10a"; }
+
+.fa-building-lock::before {
+  content: "\e4d6"; }
+
+.fa-pizza-slice::before {
+  content: "\f818"; }
+
+.fa-money-bill-wave::before {
+  content: "\f53a"; }
+
+.fa-chart-area::before {
+  content: "\f1fe"; }
+
+.fa-area-chart::before {
+  content: "\f1fe"; }
+
+.fa-house-flag::before {
+  content: "\e50d"; }
+
+.fa-person-circle-minus::before {
+  content: "\e540"; }
+
+.fa-ban::before {
+  content: "\f05e"; }
+
+.fa-cancel::before {
+  content: "\f05e"; }
+
+.fa-camera-rotate::before {
+  content: "\e0d8"; }
+
+.fa-spray-can-sparkles::before {
+  content: "\f5d0"; }
+
+.fa-air-freshener::before {
+  content: "\f5d0"; }
+
+.fa-star::before {
+  content: "\f005"; }
+
+.fa-repeat::before {
+  content: "\f363"; }
+
+.fa-cross::before {
+  content: "\f654"; }
+
+.fa-box::before {
+  content: "\f466"; }
+
+.fa-venus-mars::before {
+  content: "\f228"; }
+
+.fa-arrow-pointer::before {
+  content: "\f245"; }
+
+.fa-mouse-pointer::before {
+  content: "\f245"; }
+
+.fa-maximize::before {
+  content: "\f31e"; }
+
+.fa-expand-arrows-alt::before {
+  content: "\f31e"; }
+
+.fa-charging-station::before {
+  content: "\f5e7"; }
+
+.fa-shapes::before {
+  content: "\f61f"; }
+
+.fa-triangle-circle-square::before {
+  content: "\f61f"; }
+
+.fa-shuffle::before {
+  content: "\f074"; }
+
+.fa-random::before {
+  content: "\f074"; }
+
+.fa-person-running::before {
+  content: "\f70c"; }
+
+.fa-running::before {
+  content: "\f70c"; }
+
+.fa-mobile-retro::before {
+  content: "\e527"; }
+
+.fa-grip-lines-vertical::before {
+  content: "\f7a5"; }
+
+.fa-spider::before {
+  content: "\f717"; }
+
+.fa-hands-bound::before {
+  content: "\e4f9"; }
+
+.fa-file-invoice-dollar::before {
+  content: "\f571"; }
+
+.fa-plane-circle-exclamation::before {
+  content: "\e556"; }
+
+.fa-x-ray::before {
+  content: "\f497"; }
+
+.fa-spell-check::before {
+  content: "\f891"; }
+
+.fa-slash::before {
+  content: "\f715"; }
+
+.fa-computer-mouse::before {
+  content: "\f8cc"; }
+
+.fa-mouse::before {
+  content: "\f8cc"; }
+
+.fa-arrow-right-to-bracket::before {
+  content: "\f090"; }
+
+.fa-sign-in::before {
+  content: "\f090"; }
+
+.fa-shop-slash::before {
+  content: "\e070"; }
+
+.fa-store-alt-slash::before {
+  content: "\e070"; }
+
+.fa-server::before {
+  content: "\f233"; }
+
+.fa-virus-covid-slash::before {
+  content: "\e4a9"; }
+
+.fa-shop-lock::before {
+  content: "\e4a5"; }
+
+.fa-hourglass-start::before {
+  content: "\f251"; }
+
+.fa-hourglass-1::before {
+  content: "\f251"; }
+
+.fa-blender-phone::before {
+  content: "\f6b6"; }
+
+.fa-building-wheat::before {
+  content: "\e4db"; }
+
+.fa-person-breastfeeding::before {
+  content: "\e53a"; }
+
+.fa-right-to-bracket::before {
+  content: "\f2f6"; }
+
+.fa-sign-in-alt::before {
+  content: "\f2f6"; }
+
+.fa-venus::before {
+  content: "\f221"; }
+
+.fa-passport::before {
+  content: "\f5ab"; }
+
+.fa-heart-pulse::before {
+  content: "\f21e"; }
+
+.fa-heartbeat::before {
+  content: "\f21e"; }
+
+.fa-people-carry-box::before {
+  content: "\f4ce"; }
+
+.fa-people-carry::before {
+  content: "\f4ce"; }
+
+.fa-temperature-high::before {
+  content: "\f769"; }
+
+.fa-microchip::before {
+  content: "\f2db"; }
+
+.fa-crown::before {
+  content: "\f521"; }
+
+.fa-weight-hanging::before {
+  content: "\f5cd"; }
+
+.fa-xmarks-lines::before {
+  content: "\e59a"; }
+
+.fa-file-prescription::before {
+  content: "\f572"; }
+
+.fa-weight-scale::before {
+  content: "\f496"; }
+
+.fa-weight::before {
+  content: "\f496"; }
+
+.fa-user-group::before {
+  content: "\f500"; }
+
+.fa-user-friends::before {
+  content: "\f500"; }
+
+.fa-arrow-up-a-z::before {
+  content: "\f15e"; }
+
+.fa-sort-alpha-up::before {
+  content: "\f15e"; }
+
+.fa-chess-knight::before {
+  content: "\f441"; }
+
+.fa-face-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-laugh-squint::before {
+  content: "\f59b"; }
+
+.fa-wheelchair::before {
+  content: "\f193"; }
+
+.fa-circle-arrow-up::before {
+  content: "\f0aa"; }
+
+.fa-arrow-circle-up::before {
+  content: "\f0aa"; }
+
+.fa-toggle-on::before {
+  content: "\f205"; }
+
+.fa-person-walking::before {
+  content: "\f554"; }
+
+.fa-walking::before {
+  content: "\f554"; }
+
+.fa-l::before {
+  content: "\4c"; }
+
+.fa-fire::before {
+  content: "\f06d"; }
+
+.fa-bed-pulse::before {
+  content: "\f487"; }
+
+.fa-procedures::before {
+  content: "\f487"; }
+
+.fa-shuttle-space::before {
+  content: "\f197"; }
+
+.fa-space-shuttle::before {
+  content: "\f197"; }
+
+.fa-face-laugh::before {
+  content: "\f599"; }
+
+.fa-laugh::before {
+  content: "\f599"; }
+
+.fa-folder-open::before {
+  content: "\f07c"; }
+
+.fa-heart-circle-plus::before {
+  content: "\e500"; }
+
+.fa-code-fork::before {
+  content: "\e13b"; }
+
+.fa-city::before {
+  content: "\f64f"; }
+
+.fa-microphone-lines::before {
+  content: "\f3c9"; }
+
+.fa-microphone-alt::before {
+  content: "\f3c9"; }
+
+.fa-pepper-hot::before {
+  content: "\f816"; }
+
+.fa-unlock::before {
+  content: "\f09c"; }
+
+.fa-colon-sign::before {
+  content: "\e140"; }
+
+.fa-headset::before {
+  content: "\f590"; }
+
+.fa-store-slash::before {
+  content: "\e071"; }
+
+.fa-road-circle-xmark::before {
+  content: "\e566"; }
+
+.fa-user-minus::before {
+  content: "\f503"; }
+
+.fa-mars-stroke-up::before {
+  content: "\f22a"; }
+
+.fa-mars-stroke-v::before {
+  content: "\f22a"; }
+
+.fa-champagne-glasses::before {
+  content: "\f79f"; }
+
+.fa-glass-cheers::before {
+  content: "\f79f"; }
+
+.fa-clipboard::before {
+  content: "\f328"; }
+
+.fa-house-circle-exclamation::before {
+  content: "\e50a"; }
+
+.fa-file-arrow-up::before {
+  content: "\f574"; }
+
+.fa-file-upload::before {
+  content: "\f574"; }
+
+.fa-wifi::before {
+  content: "\f1eb"; }
+
+.fa-wifi-3::before {
+  content: "\f1eb"; }
+
+.fa-wifi-strong::before {
+  content: "\f1eb"; }
+
+.fa-bath::before {
+  content: "\f2cd"; }
+
+.fa-bathtub::before {
+  content: "\f2cd"; }
+
+.fa-underline::before {
+  content: "\f0cd"; }
+
+.fa-user-pen::before {
+  content: "\f4ff"; }
+
+.fa-user-edit::before {
+  content: "\f4ff"; }
+
+.fa-signature::before {
+  content: "\f5b7"; }
+
+.fa-stroopwafel::before {
+  content: "\f551"; }
+
+.fa-bold::before {
+  content: "\f032"; }
+
+.fa-anchor-lock::before {
+  content: "\e4ad"; }
+
+.fa-building-ngo::before {
+  content: "\e4d7"; }
+
+.fa-manat-sign::before {
+  content: "\e1d5"; }
+
+.fa-not-equal::before {
+  content: "\f53e"; }
+
+.fa-border-top-left::before {
+  content: "\f853"; }
+
+.fa-border-style::before {
+  content: "\f853"; }
+
+.fa-map-location-dot::before {
+  content: "\f5a0"; }
+
+.fa-map-marked-alt::before {
+  content: "\f5a0"; }
+
+.fa-jedi::before {
+  content: "\f669"; }
+
+.fa-square-poll-vertical::before {
+  content: "\f681"; }
+
+.fa-poll::before {
+  content: "\f681"; }
+
+.fa-mug-hot::before {
+  content: "\f7b6"; }
+
+.fa-car-battery::before {
+  content: "\f5df"; }
+
+.fa-battery-car::before {
+  content: "\f5df"; }
+
+.fa-gift::before {
+  content: "\f06b"; }
+
+.fa-dice-two::before {
+  content: "\f528"; }
+
+.fa-chess-queen::before {
+  content: "\f445"; }
+
+.fa-glasses::before {
+  content: "\f530"; }
+
+.fa-chess-board::before {
+  content: "\f43c"; }
+
+.fa-building-circle-check::before {
+  content: "\e4d2"; }
+
+.fa-person-chalkboard::before {
+  content: "\e53d"; }
+
+.fa-mars-stroke-right::before {
+  content: "\f22b"; }
+
+.fa-mars-stroke-h::before {
+  content: "\f22b"; }
+
+.fa-hand-back-fist::before {
+  content: "\f255"; }
+
+.fa-hand-rock::before {
+  content: "\f255"; }
+
+.fa-square-caret-up::before {
+  content: "\f151"; }
+
+.fa-caret-square-up::before {
+  content: "\f151"; }
+
+.fa-cloud-showers-water::before {
+  content: "\e4e4"; }
+
+.fa-chart-bar::before {
+  content: "\f080"; }
+
+.fa-bar-chart::before {
+  content: "\f080"; }
+
+.fa-hands-bubbles::before {
+  content: "\e05e"; }
+
+.fa-hands-wash::before {
+  content: "\e05e"; }
+
+.fa-less-than-equal::before {
+  content: "\f537"; }
+
+.fa-train::before {
+  content: "\f238"; }
+
+.fa-eye-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-low-vision::before {
+  content: "\f2a8"; }
+
+.fa-crow::before {
+  content: "\f520"; }
+
+.fa-sailboat::before {
+  content: "\e445"; }
+
+.fa-window-restore::before {
+  content: "\f2d2"; }
+
+.fa-square-plus::before {
+  content: "\f0fe"; }
+
+.fa-plus-square::before {
+  content: "\f0fe"; }
+
+.fa-torii-gate::before {
+  content: "\f6a1"; }
+
+.fa-frog::before {
+  content: "\f52e"; }
+
+.fa-bucket::before {
+  content: "\e4cf"; }
+
+.fa-image::before {
+  content: "\f03e"; }
+
+.fa-microphone::before {
+  content: "\f130"; }
+
+.fa-cow::before {
+  content: "\f6c8"; }
+
+.fa-caret-up::before {
+  content: "\f0d8"; }
+
+.fa-screwdriver::before {
+  content: "\f54a"; }
+
+.fa-folder-closed::before {
+  content: "\e185"; }
+
+.fa-house-tsunami::before {
+  content: "\e515"; }
+
+.fa-square-nfi::before {
+  content: "\e576"; }
+
+.fa-arrow-up-from-ground-water::before {
+  content: "\e4b5"; }
+
+.fa-martini-glass::before {
+  content: "\f57b"; }
+
+.fa-glass-martini-alt::before {
+  content: "\f57b"; }
+
+.fa-rotate-left::before {
+  content: "\f2ea"; }
+
+.fa-rotate-back::before {
+  content: "\f2ea"; }
+
+.fa-rotate-backward::before {
+  content: "\f2ea"; }
+
+.fa-undo-alt::before {
+  content: "\f2ea"; }
+
+.fa-table-columns::before {
+  content: "\f0db"; }
+
+.fa-columns::before {
+  content: "\f0db"; }
+
+.fa-lemon::before {
+  content: "\f094"; }
+
+.fa-head-side-mask::before {
+  content: "\e063"; }
+
+.fa-handshake::before {
+  content: "\f2b5"; }
+
+.fa-gem::before {
+  content: "\f3a5"; }
+
+.fa-dolly::before {
+  content: "\f472"; }
+
+.fa-dolly-box::before {
+  content: "\f472"; }
+
+.fa-smoking::before {
+  content: "\f48d"; }
+
+.fa-minimize::before {
+  content: "\f78c"; }
+
+.fa-compress-arrows-alt::before {
+  content: "\f78c"; }
+
+.fa-monument::before {
+  content: "\f5a6"; }
+
+.fa-snowplow::before {
+  content: "\f7d2"; }
+
+.fa-angles-right::before {
+  content: "\f101"; }
+
+.fa-angle-double-right::before {
+  content: "\f101"; }
+
+.fa-cannabis::before {
+  content: "\f55f"; }
+
+.fa-circle-play::before {
+  content: "\f144"; }
+
+.fa-play-circle::before {
+  content: "\f144"; }
+
+.fa-tablets::before {
+  content: "\f490"; }
+
+.fa-ethernet::before {
+  content: "\f796"; }
+
+.fa-euro-sign::before {
+  content: "\f153"; }
+
+.fa-eur::before {
+  content: "\f153"; }
+
+.fa-euro::before {
+  content: "\f153"; }
+
+.fa-chair::before {
+  content: "\f6c0"; }
+
+.fa-circle-check::before {
+  content: "\f058"; }
+
+.fa-check-circle::before {
+  content: "\f058"; }
+
+.fa-circle-stop::before {
+  content: "\f28d"; }
+
+.fa-stop-circle::before {
+  content: "\f28d"; }
+
+.fa-compass-drafting::before {
+  content: "\f568"; }
+
+.fa-drafting-compass::before {
+  content: "\f568"; }
+
+.fa-plate-wheat::before {
+  content: "\e55a"; }
+
+.fa-icicles::before {
+  content: "\f7ad"; }
+
+.fa-person-shelter::before {
+  content: "\e54f"; }
+
+.fa-neuter::before {
+  content: "\f22c"; }
+
+.fa-id-badge::before {
+  content: "\f2c1"; }
+
+.fa-marker::before {
+  content: "\f5a1"; }
+
+.fa-face-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-laugh-beam::before {
+  content: "\f59a"; }
+
+.fa-helicopter-symbol::before {
+  content: "\e502"; }
+
+.fa-universal-access::before {
+  content: "\f29a"; }
+
+.fa-circle-chevron-up::before {
+  content: "\f139"; }
+
+.fa-chevron-circle-up::before {
+  content: "\f139"; }
+
+.fa-lari-sign::before {
+  content: "\e1c8"; }
+
+.fa-volcano::before {
+  content: "\f770"; }
+
+.fa-person-walking-dashed-line-arrow-right::before {
+  content: "\e553"; }
+
+.fa-sterling-sign::before {
+  content: "\f154"; }
+
+.fa-gbp::before {
+  content: "\f154"; }
+
+.fa-pound-sign::before {
+  content: "\f154"; }
+
+.fa-viruses::before {
+  content: "\e076"; }
+
+.fa-square-person-confined::before {
+  content: "\e577"; }
+
+.fa-user-tie::before {
+  content: "\f508"; }
+
+.fa-arrow-down-long::before {
+  content: "\f175"; }
+
+.fa-long-arrow-down::before {
+  content: "\f175"; }
+
+.fa-tent-arrow-down-to-line::before {
+  content: "\e57e"; }
+
+.fa-certificate::before {
+  content: "\f0a3"; }
+
+.fa-reply-all::before {
+  content: "\f122"; }
+
+.fa-mail-reply-all::before {
+  content: "\f122"; }
+
+.fa-suitcase::before {
+  content: "\f0f2"; }
+
+.fa-person-skating::before {
+  content: "\f7c5"; }
+
+.fa-skating::before {
+  content: "\f7c5"; }
+
+.fa-filter-circle-dollar::before {
+  content: "\f662"; }
+
+.fa-funnel-dollar::before {
+  content: "\f662"; }
+
+.fa-camera-retro::before {
+  content: "\f083"; }
+
+.fa-circle-arrow-down::before {
+  content: "\f0ab"; }
+
+.fa-arrow-circle-down::before {
+  content: "\f0ab"; }
+
+.fa-file-import::before {
+  content: "\f56f"; }
+
+.fa-arrow-right-to-file::before {
+  content: "\f56f"; }
+
+.fa-square-arrow-up-right::before {
+  content: "\f14c"; }
+
+.fa-external-link-square::before {
+  content: "\f14c"; }
+
+.fa-box-open::before {
+  content: "\f49e"; }
+
+.fa-scroll::before {
+  content: "\f70e"; }
+
+.fa-spa::before {
+  content: "\f5bb"; }
+
+.fa-location-pin-lock::before {
+  content: "\e51f"; }
+
+.fa-pause::before {
+  content: "\f04c"; }
+
+.fa-hill-avalanche::before {
+  content: "\e507"; }
+
+.fa-temperature-empty::before {
+  content: "\f2cb"; }
+
+.fa-temperature-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-0::before {
+  content: "\f2cb"; }
+
+.fa-thermometer-empty::before {
+  content: "\f2cb"; }
+
+.fa-bomb::before {
+  content: "\f1e2"; }
+
+.fa-registered::before {
+  content: "\f25d"; }
+
+.fa-address-card::before {
+  content: "\f2bb"; }
+
+.fa-contact-card::before {
+  content: "\f2bb"; }
+
+.fa-vcard::before {
+  content: "\f2bb"; }
+
+.fa-scale-unbalanced-flip::before {
+  content: "\f516"; }
+
+.fa-balance-scale-right::before {
+  content: "\f516"; }
+
+.fa-subscript::before {
+  content: "\f12c"; }
+
+.fa-diamond-turn-right::before {
+  content: "\f5eb"; }
+
+.fa-directions::before {
+  content: "\f5eb"; }
+
+.fa-burst::before {
+  content: "\e4dc"; }
+
+.fa-house-laptop::before {
+  content: "\e066"; }
+
+.fa-laptop-house::before {
+  content: "\e066"; }
+
+.fa-face-tired::before {
+  content: "\f5c8"; }
+
+.fa-tired::before {
+  content: "\f5c8"; }
+
+.fa-money-bills::before {
+  content: "\e1f3"; }
+
+.fa-smog::before {
+  content: "\f75f"; }
+
+.fa-crutch::before {
+  content: "\f7f7"; }
+
+.fa-cloud-arrow-up::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload::before {
+  content: "\f0ee"; }
+
+.fa-cloud-upload-alt::before {
+  content: "\f0ee"; }
+
+.fa-palette::before {
+  content: "\f53f"; }
+
+.fa-arrows-turn-right::before {
+  content: "\e4c0"; }
+
+.fa-vest::before {
+  content: "\e085"; }
+
+.fa-ferry::before {
+  content: "\e4ea"; }
+
+.fa-arrows-down-to-people::before {
+  content: "\e4b9"; }
+
+.fa-seedling::before {
+  content: "\f4d8"; }
+
+.fa-sprout::before {
+  content: "\f4d8"; }
+
+.fa-left-right::before {
+  content: "\f337"; }
+
+.fa-arrows-alt-h::before {
+  content: "\f337"; }
+
+.fa-boxes-packing::before {
+  content: "\e4c7"; }
+
+.fa-circle-arrow-left::before {
+  content: "\f0a8"; }
+
+.fa-arrow-circle-left::before {
+  content: "\f0a8"; }
+
+.fa-group-arrows-rotate::before {
+  content: "\e4f6"; }
+
+.fa-bowl-food::before {
+  content: "\e4c6"; }
+
+.fa-candy-cane::before {
+  content: "\f786"; }
+
+.fa-arrow-down-wide-short::before {
+  content: "\f160"; }
+
+.fa-sort-amount-asc::before {
+  content: "\f160"; }
+
+.fa-sort-amount-down::before {
+  content: "\f160"; }
+
+.fa-cloud-bolt::before {
+  content: "\f76c"; }
+
+.fa-thunderstorm::before {
+  content: "\f76c"; }
+
+.fa-text-slash::before {
+  content: "\f87d"; }
+
+.fa-remove-format::before {
+  content: "\f87d"; }
+
+.fa-face-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-smile-wink::before {
+  content: "\f4da"; }
+
+.fa-file-word::before {
+  content: "\f1c2"; }
+
+.fa-file-powerpoint::before {
+  content: "\f1c4"; }
+
+.fa-arrows-left-right::before {
+  content: "\f07e"; }
+
+.fa-arrows-h::before {
+  content: "\f07e"; }
+
+.fa-house-lock::before {
+  content: "\e510"; }
+
+.fa-cloud-arrow-down::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download::before {
+  content: "\f0ed"; }
+
+.fa-cloud-download-alt::before {
+  content: "\f0ed"; }
+
+.fa-children::before {
+  content: "\e4e1"; }
+
+.fa-chalkboard::before {
+  content: "\f51b"; }
+
+.fa-blackboard::before {
+  content: "\f51b"; }
+
+.fa-user-large-slash::before {
+  content: "\f4fa"; }
+
+.fa-user-alt-slash::before {
+  content: "\f4fa"; }
+
+.fa-envelope-open::before {
+  content: "\f2b6"; }
+
+.fa-handshake-simple-slash::before {
+  content: "\e05f"; }
+
+.fa-handshake-alt-slash::before {
+  content: "\e05f"; }
+
+.fa-mattress-pillow::before {
+  content: "\e525"; }
+
+.fa-guarani-sign::before {
+  content: "\e19a"; }
+
+.fa-arrows-rotate::before {
+  content: "\f021"; }
+
+.fa-refresh::before {
+  content: "\f021"; }
+
+.fa-sync::before {
+  content: "\f021"; }
+
+.fa-fire-extinguisher::before {
+  content: "\f134"; }
+
+.fa-cruzeiro-sign::before {
+  content: "\e152"; }
+
+.fa-greater-than-equal::before {
+  content: "\f532"; }
+
+.fa-shield-halved::before {
+  content: "\f3ed"; }
+
+.fa-shield-alt::before {
+  content: "\f3ed"; }
+
+.fa-book-atlas::before {
+  content: "\f558"; }
+
+.fa-atlas::before {
+  content: "\f558"; }
+
+.fa-virus::before {
+  content: "\e074"; }
+
+.fa-envelope-circle-check::before {
+  content: "\e4e8"; }
+
+.fa-layer-group::before {
+  content: "\f5fd"; }
+
+.fa-arrows-to-dot::before {
+  content: "\e4be"; }
+
+.fa-archway::before {
+  content: "\f557"; }
+
+.fa-heart-circle-check::before {
+  content: "\e4fd"; }
+
+.fa-house-chimney-crack::before {
+  content: "\f6f1"; }
+
+.fa-house-damage::before {
+  content: "\f6f1"; }
+
+.fa-file-zipper::before {
+  content: "\f1c6"; }
+
+.fa-file-archive::before {
+  content: "\f1c6"; }
+
+.fa-square::before {
+  content: "\f0c8"; }
+
+.fa-martini-glass-empty::before {
+  content: "\f000"; }
+
+.fa-glass-martini::before {
+  content: "\f000"; }
+
+.fa-couch::before {
+  content: "\f4b8"; }
+
+.fa-cedi-sign::before {
+  content: "\e0df"; }
+
+.fa-italic::before {
+  content: "\f033"; }
+
+.fa-church::before {
+  content: "\f51d"; }
+
+.fa-comments-dollar::before {
+  content: "\f653"; }
+
+.fa-democrat::before {
+  content: "\f747"; }
+
+.fa-z::before {
+  content: "\5a"; }
+
+.fa-person-skiing::before {
+  content: "\f7c9"; }
+
+.fa-skiing::before {
+  content: "\f7c9"; }
+
+.fa-road-lock::before {
+  content: "\e567"; }
+
+.fa-a::before {
+  content: "\41"; }
+
+.fa-temperature-arrow-down::before {
+  content: "\e03f"; }
+
+.fa-temperature-down::before {
+  content: "\e03f"; }
+
+.fa-feather-pointed::before {
+  content: "\f56b"; }
+
+.fa-feather-alt::before {
+  content: "\f56b"; }
+
+.fa-p::before {
+  content: "\50"; }
+
+.fa-snowflake::before {
+  content: "\f2dc"; }
+
+.fa-newspaper::before {
+  content: "\f1ea"; }
+
+.fa-rectangle-ad::before {
+  content: "\f641"; }
+
+.fa-ad::before {
+  content: "\f641"; }
+
+.fa-circle-arrow-right::before {
+  content: "\f0a9"; }
+
+.fa-arrow-circle-right::before {
+  content: "\f0a9"; }
+
+.fa-filter-circle-xmark::before {
+  content: "\e17b"; }
+
+.fa-locust::before {
+  content: "\e520"; }
+
+.fa-sort::before {
+  content: "\f0dc"; }
+
+.fa-unsorted::before {
+  content: "\f0dc"; }
+
+.fa-list-ol::before {
+  content: "\f0cb"; }
+
+.fa-list-1-2::before {
+  content: "\f0cb"; }
+
+.fa-list-numeric::before {
+  content: "\f0cb"; }
+
+.fa-person-dress-burst::before {
+  content: "\e544"; }
+
+.fa-money-check-dollar::before {
+  content: "\f53d"; }
+
+.fa-money-check-alt::before {
+  content: "\f53d"; }
+
+.fa-vector-square::before {
+  content: "\f5cb"; }
+
+.fa-bread-slice::before {
+  content: "\f7ec"; }
+
+.fa-language::before {
+  content: "\f1ab"; }
+
+.fa-face-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-kiss-wink-heart::before {
+  content: "\f598"; }
+
+.fa-filter::before {
+  content: "\f0b0"; }
+
+.fa-question::before {
+  content: "\3f"; }
+
+.fa-file-signature::before {
+  content: "\f573"; }
+
+.fa-up-down-left-right::before {
+  content: "\f0b2"; }
+
+.fa-arrows-alt::before {
+  content: "\f0b2"; }
+
+.fa-house-chimney-user::before {
+  content: "\e065"; }
+
+.fa-hand-holding-heart::before {
+  content: "\f4be"; }
+
+.fa-puzzle-piece::before {
+  content: "\f12e"; }
+
+.fa-money-check::before {
+  content: "\f53c"; }
+
+.fa-star-half-stroke::before {
+  content: "\f5c0"; }
+
+.fa-star-half-alt::before {
+  content: "\f5c0"; }
+
+.fa-code::before {
+  content: "\f121"; }
+
+.fa-whiskey-glass::before {
+  content: "\f7a0"; }
+
+.fa-glass-whiskey::before {
+  content: "\f7a0"; }
+
+.fa-building-circle-exclamation::before {
+  content: "\e4d3"; }
+
+.fa-magnifying-glass-chart::before {
+  content: "\e522"; }
+
+.fa-arrow-up-right-from-square::before {
+  content: "\f08e"; }
+
+.fa-external-link::before {
+  content: "\f08e"; }
+
+.fa-cubes-stacked::before {
+  content: "\e4e6"; }
+
+.fa-won-sign::before {
+  content: "\f159"; }
+
+.fa-krw::before {
+  content: "\f159"; }
+
+.fa-won::before {
+  content: "\f159"; }
+
+.fa-virus-covid::before {
+  content: "\e4a8"; }
+
+.fa-austral-sign::before {
+  content: "\e0a9"; }
+
+.fa-f::before {
+  content: "\46"; }
+
+.fa-leaf::before {
+  content: "\f06c"; }
+
+.fa-road::before {
+  content: "\f018"; }
+
+.fa-taxi::before {
+  content: "\f1ba"; }
+
+.fa-cab::before {
+  content: "\f1ba"; }
+
+.fa-person-circle-plus::before {
+  content: "\e541"; }
+
+.fa-chart-pie::before {
+  content: "\f200"; }
+
+.fa-pie-chart::before {
+  content: "\f200"; }
+
+.fa-bolt-lightning::before {
+  content: "\e0b7"; }
+
+.fa-sack-xmark::before {
+  content: "\e56a"; }
+
+.fa-file-excel::before {
+  content: "\f1c3"; }
+
+.fa-file-contract::before {
+  content: "\f56c"; }
+
+.fa-fish-fins::before {
+  content: "\e4f2"; }
+
+.fa-building-flag::before {
+  content: "\e4d5"; }
+
+.fa-face-grin-beam::before {
+  content: "\f582"; }
+
+.fa-grin-beam::before {
+  content: "\f582"; }
+
+.fa-object-ungroup::before {
+  content: "\f248"; }
+
+.fa-poop::before {
+  content: "\f619"; }
+
+.fa-location-pin::before {
+  content: "\f041"; }
+
+.fa-map-marker::before {
+  content: "\f041"; }
+
+.fa-kaaba::before {
+  content: "\f66b"; }
+
+.fa-toilet-paper::before {
+  content: "\f71e"; }
+
+.fa-helmet-safety::before {
+  content: "\f807"; }
+
+.fa-hard-hat::before {
+  content: "\f807"; }
+
+.fa-hat-hard::before {
+  content: "\f807"; }
+
+.fa-eject::before {
+  content: "\f052"; }
+
+.fa-circle-right::before {
+  content: "\f35a"; }
+
+.fa-arrow-alt-circle-right::before {
+  content: "\f35a"; }
+
+.fa-plane-circle-check::before {
+  content: "\e555"; }
+
+.fa-face-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-meh-rolling-eyes::before {
+  content: "\f5a5"; }
+
+.fa-object-group::before {
+  content: "\f247"; }
+
+.fa-chart-line::before {
+  content: "\f201"; }
+
+.fa-line-chart::before {
+  content: "\f201"; }
+
+.fa-mask-ventilator::before {
+  content: "\e524"; }
+
+.fa-arrow-right::before {
+  content: "\f061"; }
+
+.fa-signs-post::before {
+  content: "\f277"; }
+
+.fa-map-signs::before {
+  content: "\f277"; }
+
+.fa-cash-register::before {
+  content: "\f788"; }
+
+.fa-person-circle-question::before {
+  content: "\e542"; }
+
+.fa-h::before {
+  content: "\48"; }
+
+.fa-tarp::before {
+  content: "\e57b"; }
+
+.fa-screwdriver-wrench::before {
+  content: "\f7d9"; }
+
+.fa-tools::before {
+  content: "\f7d9"; }
+
+.fa-arrows-to-eye::before {
+  content: "\e4bf"; }
+
+.fa-plug-circle-bolt::before {
+  content: "\e55b"; }
+
+.fa-heart::before {
+  content: "\f004"; }
+
+.fa-mars-and-venus::before {
+  content: "\f224"; }
+
+.fa-house-user::before {
+  content: "\e1b0"; }
+
+.fa-home-user::before {
+  content: "\e1b0"; }
+
+.fa-dumpster-fire::before {
+  content: "\f794"; }
+
+.fa-house-crack::before {
+  content: "\e3b1"; }
+
+.fa-martini-glass-citrus::before {
+  content: "\f561"; }
+
+.fa-cocktail::before {
+  content: "\f561"; }
+
+.fa-face-surprise::before {
+  content: "\f5c2"; }
+
+.fa-surprise::before {
+  content: "\f5c2"; }
+
+.fa-bottle-water::before {
+  content: "\e4c5"; }
+
+.fa-circle-pause::before {
+  content: "\f28b"; }
+
+.fa-pause-circle::before {
+  content: "\f28b"; }
+
+.fa-toilet-paper-slash::before {
+  content: "\e072"; }
+
+.fa-apple-whole::before {
+  content: "\f5d1"; }
+
+.fa-apple-alt::before {
+  content: "\f5d1"; }
+
+.fa-kitchen-set::before {
+  content: "\e51a"; }
+
+.fa-r::before {
+  content: "\52"; }
+
+.fa-temperature-quarter::before {
+  content: "\f2ca"; }
+
+.fa-temperature-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-1::before {
+  content: "\f2ca"; }
+
+.fa-thermometer-quarter::before {
+  content: "\f2ca"; }
+
+.fa-cube::before {
+  content: "\f1b2"; }
+
+.fa-bitcoin-sign::before {
+  content: "\e0b4"; }
+
+.fa-shield-dog::before {
+  content: "\e573"; }
+
+.fa-solar-panel::before {
+  content: "\f5ba"; }
+
+.fa-lock-open::before {
+  content: "\f3c1"; }
+
+.fa-elevator::before {
+  content: "\e16d"; }
+
+.fa-money-bill-transfer::before {
+  content: "\e528"; }
+
+.fa-money-bill-trend-up::before {
+  content: "\e529"; }
+
+.fa-house-flood-water-circle-arrow-right::before {
+  content: "\e50f"; }
+
+.fa-square-poll-horizontal::before {
+  content: "\f682"; }
+
+.fa-poll-h::before {
+  content: "\f682"; }
+
+.fa-circle::before {
+  content: "\f111"; }
+
+.fa-backward-fast::before {
+  content: "\f049"; }
+
+.fa-fast-backward::before {
+  content: "\f049"; }
+
+.fa-recycle::before {
+  content: "\f1b8"; }
+
+.fa-user-astronaut::before {
+  content: "\f4fb"; }
+
+.fa-plane-slash::before {
+  content: "\e069"; }
+
+.fa-trademark::before {
+  content: "\f25c"; }
+
+.fa-basketball::before {
+  content: "\f434"; }
+
+.fa-basketball-ball::before {
+  content: "\f434"; }
+
+.fa-satellite-dish::before {
+  content: "\f7c0"; }
+
+.fa-circle-up::before {
+  content: "\f35b"; }
+
+.fa-arrow-alt-circle-up::before {
+  content: "\f35b"; }
+
+.fa-mobile-screen-button::before {
+  content: "\f3cd"; }
+
+.fa-mobile-alt::before {
+  content: "\f3cd"; }
+
+.fa-volume-high::before {
+  content: "\f028"; }
+
+.fa-volume-up::before {
+  content: "\f028"; }
+
+.fa-users-rays::before {
+  content: "\e593"; }
+
+.fa-wallet::before {
+  content: "\f555"; }
+
+.fa-clipboard-check::before {
+  content: "\f46c"; }
+
+.fa-file-audio::before {
+  content: "\f1c7"; }
+
+.fa-burger::before {
+  content: "\f805"; }
+
+.fa-hamburger::before {
+  content: "\f805"; }
+
+.fa-wrench::before {
+  content: "\f0ad"; }
+
+.fa-bugs::before {
+  content: "\e4d0"; }
+
+.fa-rupee-sign::before {
+  content: "\f156"; }
+
+.fa-rupee::before {
+  content: "\f156"; }
+
+.fa-file-image::before {
+  content: "\f1c5"; }
+
+.fa-circle-question::before {
+  content: "\f059"; }
+
+.fa-question-circle::before {
+  content: "\f059"; }
+
+.fa-plane-departure::before {
+  content: "\f5b0"; }
+
+.fa-handshake-slash::before {
+  content: "\e060"; }
+
+.fa-book-bookmark::before {
+  content: "\e0bb"; }
+
+.fa-code-branch::before {
+  content: "\f126"; }
+
+.fa-hat-cowboy::before {
+  content: "\f8c0"; }
+
+.fa-bridge::before {
+  content: "\e4c8"; }
+
+.fa-phone-flip::before {
+  content: "\f879"; }
+
+.fa-phone-alt::before {
+  content: "\f879"; }
+
+.fa-truck-front::before {
+  content: "\e2b7"; }
+
+.fa-cat::before {
+  content: "\f6be"; }
+
+.fa-anchor-circle-exclamation::before {
+  content: "\e4ab"; }
+
+.fa-truck-field::before {
+  content: "\e58d"; }
+
+.fa-route::before {
+  content: "\f4d7"; }
+
+.fa-clipboard-question::before {
+  content: "\e4e3"; }
+
+.fa-panorama::before {
+  content: "\e209"; }
+
+.fa-comment-medical::before {
+  content: "\f7f5"; }
+
+.fa-teeth-open::before {
+  content: "\f62f"; }
+
+.fa-file-circle-minus::before {
+  content: "\e4ed"; }
+
+.fa-tags::before {
+  content: "\f02c"; }
+
+.fa-wine-glass::before {
+  content: "\f4e3"; }
+
+.fa-forward-fast::before {
+  content: "\f050"; }
+
+.fa-fast-forward::before {
+  content: "\f050"; }
+
+.fa-face-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-meh-blank::before {
+  content: "\f5a4"; }
+
+.fa-square-parking::before {
+  content: "\f540"; }
+
+.fa-parking::before {
+  content: "\f540"; }
+
+.fa-house-signal::before {
+  content: "\e012"; }
+
+.fa-bars-progress::before {
+  content: "\f828"; }
+
+.fa-tasks-alt::before {
+  content: "\f828"; }
+
+.fa-faucet-drip::before {
+  content: "\e006"; }
+
+.fa-cart-flatbed::before {
+  content: "\f474"; }
+
+.fa-dolly-flatbed::before {
+  content: "\f474"; }
+
+.fa-ban-smoking::before {
+  content: "\f54d"; }
+
+.fa-smoking-ban::before {
+  content: "\f54d"; }
+
+.fa-terminal::before {
+  content: "\f120"; }
+
+.fa-mobile-button::before {
+  content: "\f10b"; }
+
+.fa-house-medical-flag::before {
+  content: "\e514"; }
+
+.fa-basket-shopping::before {
+  content: "\f291"; }
+
+.fa-shopping-basket::before {
+  content: "\f291"; }
+
+.fa-tape::before {
+  content: "\f4db"; }
+
+.fa-bus-simple::before {
+  content: "\f55e"; }
+
+.fa-bus-alt::before {
+  content: "\f55e"; }
+
+.fa-eye::before {
+  content: "\f06e"; }
+
+.fa-face-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-sad-cry::before {
+  content: "\f5b3"; }
+
+.fa-audio-description::before {
+  content: "\f29e"; }
+
+.fa-person-military-to-person::before {
+  content: "\e54c"; }
+
+.fa-file-shield::before {
+  content: "\e4f0"; }
+
+.fa-user-slash::before {
+  content: "\f506"; }
+
+.fa-pen::before {
+  content: "\f304"; }
+
+.fa-tower-observation::before {
+  content: "\e586"; }
+
+.fa-file-code::before {
+  content: "\f1c9"; }
+
+.fa-signal::before {
+  content: "\f012"; }
+
+.fa-signal-5::before {
+  content: "\f012"; }
+
+.fa-signal-perfect::before {
+  content: "\f012"; }
+
+.fa-bus::before {
+  content: "\f207"; }
+
+.fa-heart-circle-xmark::before {
+  content: "\e501"; }
+
+.fa-house-chimney::before {
+  content: "\e3af"; }
+
+.fa-home-lg::before {
+  content: "\e3af"; }
+
+.fa-window-maximize::before {
+  content: "\f2d0"; }
+
+.fa-face-frown::before {
+  content: "\f119"; }
+
+.fa-frown::before {
+  content: "\f119"; }
+
+.fa-prescription::before {
+  content: "\f5b1"; }
+
+.fa-shop::before {
+  content: "\f54f"; }
+
+.fa-store-alt::before {
+  content: "\f54f"; }
+
+.fa-floppy-disk::before {
+  content: "\f0c7"; }
+
+.fa-save::before {
+  content: "\f0c7"; }
+
+.fa-vihara::before {
+  content: "\f6a7"; }
+
+.fa-scale-unbalanced::before {
+  content: "\f515"; }
+
+.fa-balance-scale-left::before {
+  content: "\f515"; }
+
+.fa-sort-up::before {
+  content: "\f0de"; }
+
+.fa-sort-asc::before {
+  content: "\f0de"; }
+
+.fa-comment-dots::before {
+  content: "\f4ad"; }
+
+.fa-commenting::before {
+  content: "\f4ad"; }
+
+.fa-plant-wilt::before {
+  content: "\e5aa"; }
+
+.fa-diamond::before {
+  content: "\f219"; }
+
+.fa-face-grin-squint::before {
+  content: "\f585"; }
+
+.fa-grin-squint::before {
+  content: "\f585"; }
+
+.fa-hand-holding-dollar::before {
+  content: "\f4c0"; }
+
+.fa-hand-holding-usd::before {
+  content: "\f4c0"; }
+
+.fa-bacterium::before {
+  content: "\e05a"; }
+
+.fa-hand-pointer::before {
+  content: "\f25a"; }
+
+.fa-drum-steelpan::before {
+  content: "\f56a"; }
+
+.fa-hand-scissors::before {
+  content: "\f257"; }
+
+.fa-hands-praying::before {
+  content: "\f684"; }
+
+.fa-praying-hands::before {
+  content: "\f684"; }
+
+.fa-arrow-rotate-right::before {
+  content: "\f01e"; }
+
+.fa-arrow-right-rotate::before {
+  content: "\f01e"; }
+
+.fa-arrow-rotate-forward::before {
+  content: "\f01e"; }
+
+.fa-redo::before {
+  content: "\f01e"; }
+
+.fa-biohazard::before {
+  content: "\f780"; }
+
+.fa-location-crosshairs::before {
+  content: "\f601"; }
+
+.fa-location::before {
+  content: "\f601"; }
+
+.fa-mars-double::before {
+  content: "\f227"; }
+
+.fa-child-dress::before {
+  content: "\e59c"; }
+
+.fa-users-between-lines::before {
+  content: "\e591"; }
+
+.fa-lungs-virus::before {
+  content: "\e067"; }
+
+.fa-face-grin-tears::before {
+  content: "\f588"; }
+
+.fa-grin-tears::before {
+  content: "\f588"; }
+
+.fa-phone::before {
+  content: "\f095"; }
+
+.fa-calendar-xmark::before {
+  content: "\f273"; }
+
+.fa-calendar-times::before {
+  content: "\f273"; }
+
+.fa-child-reaching::before {
+  content: "\e59d"; }
+
+.fa-head-side-virus::before {
+  content: "\e064"; }
+
+.fa-user-gear::before {
+  content: "\f4fe"; }
+
+.fa-user-cog::before {
+  content: "\f4fe"; }
+
+.fa-arrow-up-1-9::before {
+  content: "\f163"; }
+
+.fa-sort-numeric-up::before {
+  content: "\f163"; }
+
+.fa-door-closed::before {
+  content: "\f52a"; }
+
+.fa-shield-virus::before {
+  content: "\e06c"; }
+
+.fa-dice-six::before {
+  content: "\f526"; }
+
+.fa-mosquito-net::before {
+  content: "\e52c"; }
+
+.fa-bridge-water::before {
+  content: "\e4ce"; }
+
+.fa-person-booth::before {
+  content: "\f756"; }
+
+.fa-text-width::before {
+  content: "\f035"; }
+
+.fa-hat-wizard::before {
+  content: "\f6e8"; }
+
+.fa-pen-fancy::before {
+  content: "\f5ac"; }
+
+.fa-person-digging::before {
+  content: "\f85e"; }
+
+.fa-digging::before {
+  content: "\f85e"; }
+
+.fa-trash::before {
+  content: "\f1f8"; }
+
+.fa-gauge-simple::before {
+  content: "\f629"; }
+
+.fa-gauge-simple-med::before {
+  content: "\f629"; }
+
+.fa-tachometer-average::before {
+  content: "\f629"; }
+
+.fa-book-medical::before {
+  content: "\f7e6"; }
+
+.fa-poo::before {
+  content: "\f2fe"; }
+
+.fa-quote-right::before {
+  content: "\f10e"; }
+
+.fa-quote-right-alt::before {
+  content: "\f10e"; }
+
+.fa-shirt::before {
+  content: "\f553"; }
+
+.fa-t-shirt::before {
+  content: "\f553"; }
+
+.fa-tshirt::before {
+  content: "\f553"; }
+
+.fa-cubes::before {
+  content: "\f1b3"; }
+
+.fa-divide::before {
+  content: "\f529"; }
+
+.fa-tenge-sign::before {
+  content: "\f7d7"; }
+
+.fa-tenge::before {
+  content: "\f7d7"; }
+
+.fa-headphones::before {
+  content: "\f025"; }
+
+.fa-hands-holding::before {
+  content: "\f4c2"; }
+
+.fa-hands-clapping::before {
+  content: "\e1a8"; }
+
+.fa-republican::before {
+  content: "\f75e"; }
+
+.fa-arrow-left::before {
+  content: "\f060"; }
+
+.fa-person-circle-xmark::before {
+  content: "\e543"; }
+
+.fa-ruler::before {
+  content: "\f545"; }
+
+.fa-align-left::before {
+  content: "\f036"; }
+
+.fa-dice-d6::before {
+  content: "\f6d1"; }
+
+.fa-restroom::before {
+  content: "\f7bd"; }
+
+.fa-j::before {
+  content: "\4a"; }
+
+.fa-users-viewfinder::before {
+  content: "\e595"; }
+
+.fa-file-video::before {
+  content: "\f1c8"; }
+
+.fa-up-right-from-square::before {
+  content: "\f35d"; }
+
+.fa-external-link-alt::before {
+  content: "\f35d"; }
+
+.fa-table-cells::before {
+  content: "\f00a"; }
+
+.fa-th::before {
+  content: "\f00a"; }
+
+.fa-file-pdf::before {
+  content: "\f1c1"; }
+
+.fa-book-bible::before {
+  content: "\f647"; }
+
+.fa-bible::before {
+  content: "\f647"; }
+
+.fa-o::before {
+  content: "\4f"; }
+
+.fa-suitcase-medical::before {
+  content: "\f0fa"; }
+
+.fa-medkit::before {
+  content: "\f0fa"; }
+
+.fa-user-secret::before {
+  content: "\f21b"; }
+
+.fa-otter::before {
+  content: "\f700"; }
+
+.fa-person-dress::before {
+  content: "\f182"; }
+
+.fa-female::before {
+  content: "\f182"; }
+
+.fa-comment-dollar::before {
+  content: "\f651"; }
+
+.fa-business-time::before {
+  content: "\f64a"; }
+
+.fa-briefcase-clock::before {
+  content: "\f64a"; }
+
+.fa-table-cells-large::before {
+  content: "\f009"; }
+
+.fa-th-large::before {
+  content: "\f009"; }
+
+.fa-book-tanakh::before {
+  content: "\f827"; }
+
+.fa-tanakh::before {
+  content: "\f827"; }
+
+.fa-phone-volume::before {
+  content: "\f2a0"; }
+
+.fa-volume-control-phone::before {
+  content: "\f2a0"; }
+
+.fa-hat-cowboy-side::before {
+  content: "\f8c1"; }
+
+.fa-clipboard-user::before {
+  content: "\f7f3"; }
+
+.fa-child::before {
+  content: "\f1ae"; }
+
+.fa-lira-sign::before {
+  content: "\f195"; }
+
+.fa-satellite::before {
+  content: "\f7bf"; }
+
+.fa-plane-lock::before {
+  content: "\e558"; }
+
+.fa-tag::before {
+  content: "\f02b"; }
+
+.fa-comment::before {
+  content: "\f075"; }
+
+.fa-cake-candles::before {
+  content: "\f1fd"; }
+
+.fa-birthday-cake::before {
+  content: "\f1fd"; }
+
+.fa-cake::before {
+  content: "\f1fd"; }
+
+.fa-envelope::before {
+  content: "\f0e0"; }
+
+.fa-angles-up::before {
+  content: "\f102"; }
+
+.fa-angle-double-up::before {
+  content: "\f102"; }
+
+.fa-paperclip::before {
+  content: "\f0c6"; }
+
+.fa-arrow-right-to-city::before {
+  content: "\e4b3"; }
+
+.fa-ribbon::before {
+  content: "\f4d6"; }
+
+.fa-lungs::before {
+  content: "\f604"; }
+
+.fa-arrow-up-9-1::before {
+  content: "\f887"; }
+
+.fa-sort-numeric-up-alt::before {
+  content: "\f887"; }
+
+.fa-litecoin-sign::before {
+  content: "\e1d3"; }
+
+.fa-border-none::before {
+  content: "\f850"; }
+
+.fa-circle-nodes::before {
+  content: "\e4e2"; }
+
+.fa-parachute-box::before {
+  content: "\f4cd"; }
+
+.fa-indent::before {
+  content: "\f03c"; }
+
+.fa-truck-field-un::before {
+  content: "\e58e"; }
+
+.fa-hourglass::before {
+  content: "\f254"; }
+
+.fa-hourglass-empty::before {
+  content: "\f254"; }
+
+.fa-mountain::before {
+  content: "\f6fc"; }
+
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+  content: "\f0f0"; }
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+  content: "\f0f0"; }
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+  content: "\f05a"; }
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+  content: "\f05a"; }
+
+.fa-cloud-meatball::before {
+  content: "\f73b"; }
+
+.fa-camera::before {
+  content: "\f030"; }
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+.fa-camera-alt::before {
+  content: "\f030"; }
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+.fa-square-virus::before {
+  content: "\e578"; }
+
+.fa-meteor::before {
+  content: "\f753"; }
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+.fa-car-on::before {
+  content: "\e4dd"; }
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+.fa-sleigh::before {
+  content: "\f7cc"; }
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+  content: "\f162"; }
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+  content: "\f162"; }
+
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+  content: "\f162"; }
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+  content: "\f4c1"; }
+
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+  content: "\f4c1"; }
+
+.fa-water::before {
+  content: "\f773"; }
+
+.fa-calendar-check::before {
+  content: "\f274"; }
+
+.fa-braille::before {
+  content: "\f2a1"; }
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+.fa-prescription-bottle-medical::before {
+  content: "\f486"; }
+
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+  content: "\f486"; }
+
+.fa-landmark::before {
+  content: "\f66f"; }
+
+.fa-truck::before {
+  content: "\f0d1"; }
+
+.fa-crosshairs::before {
+  content: "\f05b"; }
+
+.fa-person-cane::before {
+  content: "\e53c"; }
+
+.fa-tent::before {
+  content: "\e57d"; }
+
+.fa-vest-patches::before {
+  content: "\e086"; }
+
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+  content: "\f560"; }
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+  content: "\f15d"; }
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+  content: "\f15d"; }
+
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+  content: "\f15d"; }
+
+.fa-money-bill-wheat::before {
+  content: "\e52a"; }
+
+.fa-cookie::before {
+  content: "\f563"; }
+
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+  content: "\f0e2"; }
+
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+  content: "\f0e2"; }
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+  content: "\f0e2"; }
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+  content: "\f0e2"; }
+
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+  content: "\f0e2"; }
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+  content: "\f0a0"; }
+
+.fa-hdd::before {
+  content: "\f0a0"; }
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+.fa-face-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-grin-squint-tears::before {
+  content: "\f586"; }
+
+.fa-dumbbell::before {
+  content: "\f44b"; }
+
+.fa-rectangle-list::before {
+  content: "\f022"; }
+
+.fa-list-alt::before {
+  content: "\f022"; }
+
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+  content: "\e57c"; }
+
+.fa-house-medical-circle-check::before {
+  content: "\e511"; }
+
+.fa-person-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-skiing-nordic::before {
+  content: "\f7ca"; }
+
+.fa-calendar-plus::before {
+  content: "\f271"; }
+
+.fa-plane-arrival::before {
+  content: "\f5af"; }
+
+.fa-circle-left::before {
+  content: "\f359"; }
+
+.fa-arrow-alt-circle-left::before {
+  content: "\f359"; }
+
+.fa-train-subway::before {
+  content: "\f239"; }
+
+.fa-subway::before {
+  content: "\f239"; }
+
+.fa-chart-gantt::before {
+  content: "\e0e4"; }
+
+.fa-indian-rupee-sign::before {
+  content: "\e1bc"; }
+
+.fa-indian-rupee::before {
+  content: "\e1bc"; }
+
+.fa-inr::before {
+  content: "\e1bc"; }
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+.fa-crop-simple::before {
+  content: "\f565"; }
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+.fa-crop-alt::before {
+  content: "\f565"; }
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+.fa-money-bill-1::before {
+  content: "\f3d1"; }
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+  content: "\f3d1"; }
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+.fa-left-long::before {
+  content: "\f30a"; }
+
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+  content: "\f30a"; }
+
+.fa-dna::before {
+  content: "\f471"; }
+
+.fa-virus-slash::before {
+  content: "\e075"; }
+
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+  content: "\f068"; }
+
+.fa-subtract::before {
+  content: "\f068"; }
+
+.fa-chess::before {
+  content: "\f439"; }
+
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+  content: "\f177"; }
+
+.fa-long-arrow-left::before {
+  content: "\f177"; }
+
+.fa-plug-circle-check::before {
+  content: "\e55c"; }
+
+.fa-street-view::before {
+  content: "\f21d"; }
+
+.fa-franc-sign::before {
+  content: "\e18f"; }
+
+.fa-volume-off::before {
+  content: "\f026"; }
+
+.fa-hands-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-asl-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-hands-american-sign-language-interpreting::before {
+  content: "\f2a3"; }
+
+.fa-gear::before {
+  content: "\f013"; }
+
+.fa-cog::before {
+  content: "\f013"; }
+
+.fa-droplet-slash::before {
+  content: "\f5c7"; }
+
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+  content: "\f5c7"; }
+
+.fa-mosque::before {
+  content: "\f678"; }
+
+.fa-mosquito::before {
+  content: "\e52b"; }
+
+.fa-star-of-david::before {
+  content: "\f69a"; }
+
+.fa-person-military-rifle::before {
+  content: "\e54b"; }
+
+.fa-cart-shopping::before {
+  content: "\f07a"; }
+
+.fa-shopping-cart::before {
+  content: "\f07a"; }
+
+.fa-vials::before {
+  content: "\f493"; }
+
+.fa-plug-circle-plus::before {
+  content: "\e55f"; }
+
+.fa-place-of-worship::before {
+  content: "\f67f"; }
+
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+  content: "\f58e"; }
+
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+  content: "\f148"; }
+
+.fa-level-up::before {
+  content: "\f148"; }
+
+.fa-u::before {
+  content: "\55"; }
+
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+  content: "\f698"; }
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+.fa-square-root-alt::before {
+  content: "\f698"; }
+
+.fa-clock::before {
+  content: "\f017"; }
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+.fa-clock-four::before {
+  content: "\f017"; }
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+.fa-backward-step::before {
+  content: "\f048"; }
+
+.fa-step-backward::before {
+  content: "\f048"; }
+
+.fa-pallet::before {
+  content: "\f482"; }
+
+.fa-faucet::before {
+  content: "\e005"; }
+
+.fa-baseball-bat-ball::before {
+  content: "\f432"; }
+
+.fa-s::before {
+  content: "\53"; }
+
+.fa-timeline::before {
+  content: "\e29c"; }
+
+.fa-keyboard::before {
+  content: "\f11c"; }
+
+.fa-caret-down::before {
+  content: "\f0d7"; }
+
+.fa-house-chimney-medical::before {
+  content: "\f7f2"; }
+
+.fa-clinic-medical::before {
+  content: "\f7f2"; }
+
+.fa-temperature-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-temperature-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-3::before {
+  content: "\f2c8"; }
+
+.fa-thermometer-three-quarters::before {
+  content: "\f2c8"; }
+
+.fa-mobile-screen::before {
+  content: "\f3cf"; }
+
+.fa-mobile-android-alt::before {
+  content: "\f3cf"; }
+
+.fa-plane-up::before {
+  content: "\e22d"; }
+
+.fa-piggy-bank::before {
+  content: "\f4d3"; }
+
+.fa-battery-half::before {
+  content: "\f242"; }
+
+.fa-battery-3::before {
+  content: "\f242"; }
+
+.fa-mountain-city::before {
+  content: "\e52e"; }
+
+.fa-coins::before {
+  content: "\f51e"; }
+
+.fa-khanda::before {
+  content: "\f66d"; }
+
+.fa-sliders::before {
+  content: "\f1de"; }
+
+.fa-sliders-h::before {
+  content: "\f1de"; }
+
+.fa-folder-tree::before {
+  content: "\f802"; }
+
+.fa-network-wired::before {
+  content: "\f6ff"; }
+
+.fa-map-pin::before {
+  content: "\f276"; }
+
+.fa-hamsa::before {
+  content: "\f665"; }
+
+.fa-cent-sign::before {
+  content: "\e3f5"; }
+
+.fa-flask::before {
+  content: "\f0c3"; }
+
+.fa-person-pregnant::before {
+  content: "\e31e"; }
+
+.fa-wand-sparkles::before {
+  content: "\f72b"; }
+
+.fa-ellipsis-vertical::before {
+  content: "\f142"; }
+
+.fa-ellipsis-v::before {
+  content: "\f142"; }
+
+.fa-ticket::before {
+  content: "\f145"; }
+
+.fa-power-off::before {
+  content: "\f011"; }
+
+.fa-right-long::before {
+  content: "\f30b"; }
+
+.fa-long-arrow-alt-right::before {
+  content: "\f30b"; }
+
+.fa-flag-usa::before {
+  content: "\f74d"; }
+
+.fa-laptop-file::before {
+  content: "\e51d"; }
+
+.fa-tty::before {
+  content: "\f1e4"; }
+
+.fa-teletype::before {
+  content: "\f1e4"; }
+
+.fa-diagram-next::before {
+  content: "\e476"; }
+
+.fa-person-rifle::before {
+  content: "\e54e"; }
+
+.fa-house-medical-circle-exclamation::before {
+  content: "\e512"; }
+
+.fa-closed-captioning::before {
+  content: "\f20a"; }
+
+.fa-person-hiking::before {
+  content: "\f6ec"; }
+
+.fa-hiking::before {
+  content: "\f6ec"; }
+
+.fa-venus-double::before {
+  content: "\f226"; }
+
+.fa-images::before {
+  content: "\f302"; }
+
+.fa-calculator::before {
+  content: "\f1ec"; }
+
+.fa-people-pulling::before {
+  content: "\e535"; }
+
+.fa-n::before {
+  content: "\4e"; }
+
+.fa-cable-car::before {
+  content: "\f7da"; }
+
+.fa-tram::before {
+  content: "\f7da"; }
+
+.fa-cloud-rain::before {
+  content: "\f73d"; }
+
+.fa-building-circle-xmark::before {
+  content: "\e4d4"; }
+
+.fa-ship::before {
+  content: "\f21a"; }
+
+.fa-arrows-down-to-line::before {
+  content: "\e4b8"; }
+
+.fa-download::before {
+  content: "\f019"; }
+
+.fa-face-grin::before {
+  content: "\f580"; }
+
+.fa-grin::before {
+  content: "\f580"; }
+
+.fa-delete-left::before {
+  content: "\f55a"; }
+
+.fa-backspace::before {
+  content: "\f55a"; }
+
+.fa-eye-dropper::before {
+  content: "\f1fb"; }
+
+.fa-eye-dropper-empty::before {
+  content: "\f1fb"; }
+
+.fa-eyedropper::before {
+  content: "\f1fb"; }
+
+.fa-file-circle-check::before {
+  content: "\e5a0"; }
+
+.fa-forward::before {
+  content: "\f04e"; }
+
+.fa-mobile::before {
+  content: "\f3ce"; }
+
+.fa-mobile-android::before {
+  content: "\f3ce"; }
+
+.fa-mobile-phone::before {
+  content: "\f3ce"; }
+
+.fa-face-meh::before {
+  content: "\f11a"; }
+
+.fa-meh::before {
+  content: "\f11a"; }
+
+.fa-align-center::before {
+  content: "\f037"; }
+
+.fa-book-skull::before {
+  content: "\f6b7"; }
+
+.fa-book-dead::before {
+  content: "\f6b7"; }
+
+.fa-id-card::before {
+  content: "\f2c2"; }
+
+.fa-drivers-license::before {
+  content: "\f2c2"; }
+
+.fa-outdent::before {
+  content: "\f03b"; }
+
+.fa-dedent::before {
+  content: "\f03b"; }
+
+.fa-heart-circle-exclamation::before {
+  content: "\e4fe"; }
+
+.fa-house::before {
+  content: "\f015"; }
+
+.fa-home::before {
+  content: "\f015"; }
+
+.fa-home-alt::before {
+  content: "\f015"; }
+
+.fa-home-lg-alt::before {
+  content: "\f015"; }
+
+.fa-calendar-week::before {
+  content: "\f784"; }
+
+.fa-laptop-medical::before {
+  content: "\f812"; }
+
+.fa-b::before {
+  content: "\42"; }
+
+.fa-file-medical::before {
+  content: "\f477"; }
+
+.fa-dice-one::before {
+  content: "\f525"; }
+
+.fa-kiwi-bird::before {
+  content: "\f535"; }
+
+.fa-arrow-right-arrow-left::before {
+  content: "\f0ec"; }
+
+.fa-exchange::before {
+  content: "\f0ec"; }
+
+.fa-rotate-right::before {
+  content: "\f2f9"; }
+
+.fa-redo-alt::before {
+  content: "\f2f9"; }
+
+.fa-rotate-forward::before {
+  content: "\f2f9"; }
+
+.fa-utensils::before {
+  content: "\f2e7"; }
+
+.fa-cutlery::before {
+  content: "\f2e7"; }
+
+.fa-arrow-up-wide-short::before {
+  content: "\f161"; }
+
+.fa-sort-amount-up::before {
+  content: "\f161"; }
+
+.fa-mill-sign::before {
+  content: "\e1ed"; }
+
+.fa-bowl-rice::before {
+  content: "\e2eb"; }
+
+.fa-skull::before {
+  content: "\f54c"; }
+
+.fa-tower-broadcast::before {
+  content: "\f519"; }
+
+.fa-broadcast-tower::before {
+  content: "\f519"; }
+
+.fa-truck-pickup::before {
+  content: "\f63c"; }
+
+.fa-up-long::before {
+  content: "\f30c"; }
+
+.fa-long-arrow-alt-up::before {
+  content: "\f30c"; }
+
+.fa-stop::before {
+  content: "\f04d"; }
+
+.fa-code-merge::before {
+  content: "\f387"; }
+
+.fa-upload::before {
+  content: "\f093"; }
+
+.fa-hurricane::before {
+  content: "\f751"; }
+
+.fa-mound::before {
+  content: "\e52d"; }
+
+.fa-toilet-portable::before {
+  content: "\e583"; }
+
+.fa-compact-disc::before {
+  content: "\f51f"; }
+
+.fa-file-arrow-down::before {
+  content: "\f56d"; }
+
+.fa-file-download::before {
+  content: "\f56d"; }
+
+.fa-caravan::before {
+  content: "\f8ff"; }
+
+.fa-shield-cat::before {
+  content: "\e572"; }
+
+.fa-bolt::before {
+  content: "\f0e7"; }
+
+.fa-zap::before {
+  content: "\f0e7"; }
+
+.fa-glass-water::before {
+  content: "\e4f4"; }
+
+.fa-oil-well::before {
+  content: "\e532"; }
+
+.fa-vault::before {
+  content: "\e2c5"; }
+
+.fa-mars::before {
+  content: "\f222"; }
+
+.fa-toilet::before {
+  content: "\f7d8"; }
+
+.fa-plane-circle-xmark::before {
+  content: "\e557"; }
+
+.fa-yen-sign::before {
+  content: "\f157"; }
+
+.fa-cny::before {
+  content: "\f157"; }
+
+.fa-jpy::before {
+  content: "\f157"; }
+
+.fa-rmb::before {
+  content: "\f157"; }
+
+.fa-yen::before {
+  content: "\f157"; }
+
+.fa-ruble-sign::before {
+  content: "\f158"; }
+
+.fa-rouble::before {
+  content: "\f158"; }
+
+.fa-rub::before {
+  content: "\f158"; }
+
+.fa-ruble::before {
+  content: "\f158"; }
+
+.fa-sun::before {
+  content: "\f185"; }
+
+.fa-guitar::before {
+  content: "\f7a6"; }
+
+.fa-face-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-laugh-wink::before {
+  content: "\f59c"; }
+
+.fa-horse-head::before {
+  content: "\f7ab"; }
+
+.fa-bore-hole::before {
+  content: "\e4c3"; }
+
+.fa-industry::before {
+  content: "\f275"; }
+
+.fa-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrow-alt-circle-down::before {
+  content: "\f358"; }
+
+.fa-arrows-turn-to-dots::before {
+  content: "\e4c1"; }
+
+.fa-florin-sign::before {
+  content: "\e184"; }
+
+.fa-arrow-down-short-wide::before {
+  content: "\f884"; }
+
+.fa-sort-amount-desc::before {
+  content: "\f884"; }
+
+.fa-sort-amount-down-alt::before {
+  content: "\f884"; }
+
+.fa-less-than::before {
+  content: "\3c"; }
+
+.fa-angle-down::before {
+  content: "\f107"; }
+
+.fa-car-tunnel::before {
+  content: "\e4de"; }
+
+.fa-head-side-cough::before {
+  content: "\e061"; }
+
+.fa-grip-lines::before {
+  content: "\f7a4"; }
+
+.fa-thumbs-down::before {
+  content: "\f165"; }
+
+.fa-user-lock::before {
+  content: "\f502"; }
+
+.fa-arrow-right-long::before {
+  content: "\f178"; }
+
+.fa-long-arrow-right::before {
+  content: "\f178"; }
+
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+  content: "\e4ac"; }
+
+.fa-ellipsis::before {
+  content: "\f141"; }
+
+.fa-ellipsis-h::before {
+  content: "\f141"; }
+
+.fa-chess-pawn::before {
+  content: "\f443"; }
+
+.fa-kit-medical::before {
+  content: "\f479"; }
+
+.fa-first-aid::before {
+  content: "\f479"; }
+
+.fa-person-through-window::before {
+  content: "\e5a9"; }
+
+.fa-toolbox::before {
+  content: "\f552"; }
+
+.fa-hands-holding-circle::before {
+  content: "\e4fb"; }
+
+.fa-bug::before {
+  content: "\f188"; }
+
+.fa-credit-card::before {
+  content: "\f09d"; }
+
+.fa-credit-card-alt::before {
+  content: "\f09d"; }
+
+.fa-car::before {
+  content: "\f1b9"; }
+
+.fa-automobile::before {
+  content: "\f1b9"; }
+
+.fa-hand-holding-hand::before {
+  content: "\e4f7"; }
+
+.fa-book-open-reader::before {
+  content: "\f5da"; }
+
+.fa-book-reader::before {
+  content: "\f5da"; }
+
+.fa-mountain-sun::before {
+  content: "\e52f"; }
+
+.fa-arrows-left-right-to-line::before {
+  content: "\e4ba"; }
+
+.fa-dice-d20::before {
+  content: "\f6cf"; }
+
+.fa-truck-droplet::before {
+  content: "\e58c"; }
+
+.fa-file-circle-xmark::before {
+  content: "\e5a1"; }
+
+.fa-temperature-arrow-up::before {
+  content: "\e040"; }
+
+.fa-temperature-up::before {
+  content: "\e040"; }
+
+.fa-medal::before {
+  content: "\f5a2"; }
+
+.fa-bed::before {
+  content: "\f236"; }
+
+.fa-square-h::before {
+  content: "\f0fd"; }
+
+.fa-h-square::before {
+  content: "\f0fd"; }
+
+.fa-podcast::before {
+  content: "\f2ce"; }
+
+.fa-temperature-full::before {
+  content: "\f2c7"; }
+
+.fa-temperature-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-4::before {
+  content: "\f2c7"; }
+
+.fa-thermometer-full::before {
+  content: "\f2c7"; }
+
+.fa-bell::before {
+  content: "\f0f3"; }
+
+.fa-superscript::before {
+  content: "\f12b"; }
+
+.fa-plug-circle-xmark::before {
+  content: "\e560"; }
+
+.fa-star-of-life::before {
+  content: "\f621"; }
+
+.fa-phone-slash::before {
+  content: "\f3dd"; }
+
+.fa-paint-roller::before {
+  content: "\f5aa"; }
+
+.fa-handshake-angle::before {
+  content: "\f4c4"; }
+
+.fa-hands-helping::before {
+  content: "\f4c4"; }
+
+.fa-location-dot::before {
+  content: "\f3c5"; }
+
+.fa-map-marker-alt::before {
+  content: "\f3c5"; }
+
+.fa-file::before {
+  content: "\f15b"; }
+
+.fa-greater-than::before {
+  content: "\3e"; }
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+  content: "\f5c4"; }
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+.fa-swimmer::before {
+  content: "\f5c4"; }
+
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+  content: "\f063"; }
+
+.fa-droplet::before {
+  content: "\f043"; }
+
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+  content: "\f043"; }
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+  content: "\f12d"; }
+
+.fa-earth-americas::before {
+  content: "\f57d"; }
+
+.fa-earth::before {
+  content: "\f57d"; }
+
+.fa-earth-america::before {
+  content: "\f57d"; }
+
+.fa-globe-americas::before {
+  content: "\f57d"; }
+
+.fa-person-burst::before {
+  content: "\e53b"; }
+
+.fa-dove::before {
+  content: "\f4ba"; }
+
+.fa-battery-empty::before {
+  content: "\f244"; }
+
+.fa-battery-0::before {
+  content: "\f244"; }
+
+.fa-socks::before {
+  content: "\f696"; }
+
+.fa-inbox::before {
+  content: "\f01c"; }
+
+.fa-section::before {
+  content: "\e447"; }
+
+.fa-gauge-high::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt::before {
+  content: "\f625"; }
+
+.fa-tachometer-alt-fast::before {
+  content: "\f625"; }
+
+.fa-envelope-open-text::before {
+  content: "\f658"; }
+
+.fa-hospital::before {
+  content: "\f0f8"; }
+
+.fa-hospital-alt::before {
+  content: "\f0f8"; }
+
+.fa-hospital-wide::before {
+  content: "\f0f8"; }
+
+.fa-wine-bottle::before {
+  content: "\f72f"; }
+
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+  content: "\f447"; }
+
+.fa-bars-staggered::before {
+  content: "\f550"; }
+
+.fa-reorder::before {
+  content: "\f550"; }
+
+.fa-stream::before {
+  content: "\f550"; }
+
+.fa-dharmachakra::before {
+  content: "\f655"; }
+
+.fa-hotdog::before {
+  content: "\f80f"; }
+
+.fa-person-walking-with-cane::before {
+  content: "\f29d"; }
+
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+  content: "\f29d"; }
+
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+  content: "\f569"; }
+
+.fa-ice-cream::before {
+  content: "\f810"; }
+
+.fa-heart-circle-bolt::before {
+  content: "\e4fc"; }
+
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+  content: "\f1ac"; }
+
+.fa-paragraph::before {
+  content: "\f1dd"; }
+
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+  content: "\f772"; }
+
+.fa-vote-yea::before {
+  content: "\f772"; }
+
+.fa-star-half::before {
+  content: "\f089"; }
+
+.fa-boxes-stacked::before {
+  content: "\f468"; }
+
+.fa-boxes::before {
+  content: "\f468"; }
+
+.fa-boxes-alt::before {
+  content: "\f468"; }
+
+.fa-link::before {
+  content: "\f0c1"; }
+
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+  content: "\f0c1"; }
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+  content: "\f2a2"; }
+
+.fa-assistive-listening-systems::before {
+  content: "\f2a2"; }
+
+.fa-tree-city::before {
+  content: "\e587"; }
+
+.fa-play::before {
+  content: "\f04b"; }
+
+.fa-font::before {
+  content: "\f031"; }
+
+.fa-rupiah-sign::before {
+  content: "\e23d"; }
+
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+  content: "\f002"; }
+
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+  content: "\f002"; }
+
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+  content: "\f45d"; }
+
+.fa-ping-pong-paddle-ball::before {
+  content: "\f45d"; }
+
+.fa-table-tennis::before {
+  content: "\f45d"; }
+
+.fa-person-dots-from-line::before {
+  content: "\f470"; }
+
+.fa-diagnoses::before {
+  content: "\f470"; }
+
+.fa-trash-can-arrow-up::before {
+  content: "\f82a"; }
+
+.fa-trash-restore-alt::before {
+  content: "\f82a"; }
+
+.fa-naira-sign::before {
+  content: "\e1f6"; }
+
+.fa-cart-arrow-down::before {
+  content: "\f218"; }
+
+.fa-walkie-talkie::before {
+  content: "\f8ef"; }
+
+.fa-file-pen::before {
+  content: "\f31c"; }
+
+.fa-file-edit::before {
+  content: "\f31c"; }
+
+.fa-receipt::before {
+  content: "\f543"; }
+
+.fa-square-pen::before {
+  content: "\f14b"; }
+
+.fa-pen-square::before {
+  content: "\f14b"; }
+
+.fa-pencil-square::before {
+  content: "\f14b"; }
+
+.fa-suitcase-rolling::before {
+  content: "\f5c1"; }
+
+.fa-person-circle-exclamation::before {
+  content: "\e53f"; }
+
+.fa-chevron-down::before {
+  content: "\f078"; }
+
+.fa-battery-full::before {
+  content: "\f240"; }
+
+.fa-battery::before {
+  content: "\f240"; }
+
+.fa-battery-5::before {
+  content: "\f240"; }
+
+.fa-skull-crossbones::before {
+  content: "\f714"; }
+
+.fa-code-compare::before {
+  content: "\e13a"; }
+
+.fa-list-ul::before {
+  content: "\f0ca"; }
+
+.fa-list-dots::before {
+  content: "\f0ca"; }
+
+.fa-school-lock::before {
+  content: "\e56f"; }
+
+.fa-tower-cell::before {
+  content: "\e585"; }
+
+.fa-down-long::before {
+  content: "\f309"; }
+
+.fa-long-arrow-alt-down::before {
+  content: "\f309"; }
+
+.fa-ranking-star::before {
+  content: "\e561"; }
+
+.fa-chess-king::before {
+  content: "\f43f"; }
+
+.fa-person-harassing::before {
+  content: "\e549"; }
+
+.fa-brazilian-real-sign::before {
+  content: "\e46c"; }
+
+.fa-landmark-dome::before {
+  content: "\f752"; }
+
+.fa-landmark-alt::before {
+  content: "\f752"; }
+
+.fa-arrow-up::before {
+  content: "\f062"; }
+
+.fa-tv::before {
+  content: "\f26c"; }
+
+.fa-television::before {
+  content: "\f26c"; }
+
+.fa-tv-alt::before {
+  content: "\f26c"; }
+
+.fa-shrimp::before {
+  content: "\e448"; }
+
+.fa-list-check::before {
+  content: "\f0ae"; }
+
+.fa-tasks::before {
+  content: "\f0ae"; }
+
+.fa-jug-detergent::before {
+  content: "\e519"; }
+
+.fa-circle-user::before {
+  content: "\f2bd"; }
+
+.fa-user-circle::before {
+  content: "\f2bd"; }
+
+.fa-user-shield::before {
+  content: "\f505"; }
+
+.fa-wind::before {
+  content: "\f72e"; }
+
+.fa-car-burst::before {
+  content: "\f5e1"; }
+
+.fa-car-crash::before {
+  content: "\f5e1"; }
+
+.fa-y::before {
+  content: "\59"; }
+
+.fa-person-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-snowboarding::before {
+  content: "\f7ce"; }
+
+.fa-truck-fast::before {
+  content: "\f48b"; }
+
+.fa-shipping-fast::before {
+  content: "\f48b"; }
+
+.fa-fish::before {
+  content: "\f578"; }
+
+.fa-user-graduate::before {
+  content: "\f501"; }
+
+.fa-circle-half-stroke::before {
+  content: "\f042"; }
+
+.fa-adjust::before {
+  content: "\f042"; }
+
+.fa-clapperboard::before {
+  content: "\e131"; }
+
+.fa-circle-radiation::before {
+  content: "\f7ba"; }
+
+.fa-radiation-alt::before {
+  content: "\f7ba"; }
+
+.fa-baseball::before {
+  content: "\f433"; }
+
+.fa-baseball-ball::before {
+  content: "\f433"; }
+
+.fa-jet-fighter-up::before {
+  content: "\e518"; }
+
+.fa-diagram-project::before {
+  content: "\f542"; }
+
+.fa-project-diagram::before {
+  content: "\f542"; }
+
+.fa-copy::before {
+  content: "\f0c5"; }
+
+.fa-volume-xmark::before {
+  content: "\f6a9"; }
+
+.fa-volume-mute::before {
+  content: "\f6a9"; }
+
+.fa-volume-times::before {
+  content: "\f6a9"; }
+
+.fa-hand-sparkles::before {
+  content: "\e05d"; }
+
+.fa-grip::before {
+  content: "\f58d"; }
+
+.fa-grip-horizontal::before {
+  content: "\f58d"; }
+
+.fa-share-from-square::before {
+  content: "\f14d"; }
+
+.fa-share-square::before {
+  content: "\f14d"; }
+
+.fa-child-combatant::before {
+  content: "\e4e0"; }
+
+.fa-child-rifle::before {
+  content: "\e4e0"; }
+
+.fa-gun::before {
+  content: "\e19b"; }
+
+.fa-square-phone::before {
+  content: "\f098"; }
+
+.fa-phone-square::before {
+  content: "\f098"; }
+
+.fa-plus::before {
+  content: "\2b"; }
+
+.fa-add::before {
+  content: "\2b"; }
+
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+  content: "\f065"; }
+
+.fa-computer::before {
+  content: "\e4e5"; }
+
+.fa-xmark::before {
+  content: "\f00d"; }
+
+.fa-close::before {
+  content: "\f00d"; }
+
+.fa-multiply::before {
+  content: "\f00d"; }
+
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+  content: "\f00d"; }
+
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+  content: "\f00d"; }
+
+.fa-arrows-up-down-left-right::before {
+  content: "\f047"; }
+
+.fa-arrows::before {
+  content: "\f047"; }
+
+.fa-chalkboard-user::before {
+  content: "\f51c"; }
+
+.fa-chalkboard-teacher::before {
+  content: "\f51c"; }
+
+.fa-peso-sign::before {
+  content: "\e222"; }
+
+.fa-building-shield::before {
+  content: "\e4d8"; }
+
+.fa-baby::before {
+  content: "\f77c"; }
+
+.fa-users-line::before {
+  content: "\e592"; }
+
+.fa-quote-left::before {
+  content: "\f10d"; }
+
+.fa-quote-left-alt::before {
+  content: "\f10d"; }
+
+.fa-tractor::before {
+  content: "\f722"; }
+
+.fa-trash-arrow-up::before {
+  content: "\f829"; }
+
+.fa-trash-restore::before {
+  content: "\f829"; }
+
+.fa-arrow-down-up-lock::before {
+  content: "\e4b0"; }
+
+.fa-lines-leaning::before {
+  content: "\e51e"; }
+
+.fa-ruler-combined::before {
+  content: "\f546"; }
+
+.fa-copyright::before {
+  content: "\f1f9"; }
+
+.fa-equals::before {
+  content: "\3d"; }
+
+.fa-blender::before {
+  content: "\f517"; }
+
+.fa-teeth::before {
+  content: "\f62e"; }
+
+.fa-shekel-sign::before {
+  content: "\f20b"; }
+
+.fa-ils::before {
+  content: "\f20b"; }
+
+.fa-shekel::before {
+  content: "\f20b"; }
+
+.fa-sheqel::before {
+  content: "\f20b"; }
+
+.fa-sheqel-sign::before {
+  content: "\f20b"; }
+
+.fa-map::before {
+  content: "\f279"; }
+
+.fa-rocket::before {
+  content: "\f135"; }
+
+.fa-photo-film::before {
+  content: "\f87c"; }
+
+.fa-photo-video::before {
+  content: "\f87c"; }
+
+.fa-folder-minus::before {
+  content: "\f65d"; }
+
+.fa-store::before {
+  content: "\f54e"; }
+
+.fa-arrow-trend-up::before {
+  content: "\e098"; }
+
+.fa-plug-circle-minus::before {
+  content: "\e55e"; }
+
+.fa-sign-hanging::before {
+  content: "\f4d9"; }
+
+.fa-sign::before {
+  content: "\f4d9"; }
+
+.fa-bezier-curve::before {
+  content: "\f55b"; }
+
+.fa-bell-slash::before {
+  content: "\f1f6"; }
+
+.fa-tablet::before {
+  content: "\f3fb"; }
+
+.fa-tablet-android::before {
+  content: "\f3fb"; }
+
+.fa-school-flag::before {
+  content: "\e56e"; }
+
+.fa-fill::before {
+  content: "\f575"; }
+
+.fa-angle-up::before {
+  content: "\f106"; }
+
+.fa-drumstick-bite::before {
+  content: "\f6d7"; }
+
+.fa-holly-berry::before {
+  content: "\f7aa"; }
+
+.fa-chevron-left::before {
+  content: "\f053"; }
+
+.fa-bacteria::before {
+  content: "\e059"; }
+
+.fa-hand-lizard::before {
+  content: "\f258"; }
+
+.fa-notdef::before {
+  content: "\e1fe"; }
+
+.fa-disease::before {
+  content: "\f7fa"; }
+
+.fa-briefcase-medical::before {
+  content: "\f469"; }
+
+.fa-genderless::before {
+  content: "\f22d"; }
+
+.fa-chevron-right::before {
+  content: "\f054"; }
+
+.fa-retweet::before {
+  content: "\f079"; }
+
+.fa-car-rear::before {
+  content: "\f5de"; }
+
+.fa-car-alt::before {
+  content: "\f5de"; }
+
+.fa-pump-soap::before {
+  content: "\e06b"; }
+
+.fa-video-slash::before {
+  content: "\f4e2"; }
+
+.fa-battery-quarter::before {
+  content: "\f243"; }
+
+.fa-battery-2::before {
+  content: "\f243"; }
+
+.fa-radio::before {
+  content: "\f8d7"; }
+
+.fa-baby-carriage::before {
+  content: "\f77d"; }
+
+.fa-carriage-baby::before {
+  content: "\f77d"; }
+
+.fa-traffic-light::before {
+  content: "\f637"; }
+
+.fa-thermometer::before {
+  content: "\f491"; }
+
+.fa-vr-cardboard::before {
+  content: "\f729"; }
+
+.fa-hand-middle-finger::before {
+  content: "\f806"; }
+
+.fa-percent::before {
+  content: "\25"; }
+
+.fa-percentage::before {
+  content: "\25"; }
+
+.fa-truck-moving::before {
+  content: "\f4df"; }
+
+.fa-glass-water-droplet::before {
+  content: "\e4f5"; }
+
+.fa-display::before {
+  content: "\e163"; }
+
+.fa-face-smile::before {
+  content: "\f118"; }
+
+.fa-smile::before {
+  content: "\f118"; }
+
+.fa-thumbtack::before {
+  content: "\f08d"; }
+
+.fa-thumb-tack::before {
+  content: "\f08d"; }
+
+.fa-trophy::before {
+  content: "\f091"; }
+
+.fa-person-praying::before {
+  content: "\f683"; }
+
+.fa-pray::before {
+  content: "\f683"; }
+
+.fa-hammer::before {
+  content: "\f6e3"; }
+
+.fa-hand-peace::before {
+  content: "\f25b"; }
+
+.fa-rotate::before {
+  content: "\f2f1"; }
+
+.fa-sync-alt::before {
+  content: "\f2f1"; }
+
+.fa-spinner::before {
+  content: "\f110"; }
+
+.fa-robot::before {
+  content: "\f544"; }
+
+.fa-peace::before {
+  content: "\f67c"; }
+
+.fa-gears::before {
+  content: "\f085"; }
+
+.fa-cogs::before {
+  content: "\f085"; }
+
+.fa-warehouse::before {
+  content: "\f494"; }
+
+.fa-arrow-up-right-dots::before {
+  content: "\e4b7"; }
+
+.fa-splotch::before {
+  content: "\f5bc"; }
+
+.fa-face-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-grin-hearts::before {
+  content: "\f584"; }
+
+.fa-dice-four::before {
+  content: "\f524"; }
+
+.fa-sim-card::before {
+  content: "\f7c4"; }
+
+.fa-transgender::before {
+  content: "\f225"; }
+
+.fa-transgender-alt::before {
+  content: "\f225"; }
+
+.fa-mercury::before {
+  content: "\f223"; }
+
+.fa-arrow-turn-down::before {
+  content: "\f149"; }
+
+.fa-level-down::before {
+  content: "\f149"; }
+
+.fa-person-falling-burst::before {
+  content: "\e547"; }
+
+.fa-award::before {
+  content: "\f559"; }
+
+.fa-ticket-simple::before {
+  content: "\f3ff"; }
+
+.fa-ticket-alt::before {
+  content: "\f3ff"; }
+
+.fa-building::before {
+  content: "\f1ad"; }
+
+.fa-angles-left::before {
+  content: "\f100"; }
+
+.fa-angle-double-left::before {
+  content: "\f100"; }
+
+.fa-qrcode::before {
+  content: "\f029"; }
+
+.fa-clock-rotate-left::before {
+  content: "\f1da"; }
+
+.fa-history::before {
+  content: "\f1da"; }
+
+.fa-face-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-grin-beam-sweat::before {
+  content: "\f583"; }
+
+.fa-file-export::before {
+  content: "\f56e"; }
+
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+  content: "\f56e"; }
+
+.fa-shield::before {
+  content: "\f132"; }
+
+.fa-shield-blank::before {
+  content: "\f132"; }
+
+.fa-arrow-up-short-wide::before {
+  content: "\f885"; }
+
+.fa-sort-amount-up-alt::before {
+  content: "\f885"; }
+
+.fa-house-medical::before {
+  content: "\e3b2"; }
+
+.fa-golf-ball-tee::before {
+  content: "\f450"; }
+
+.fa-golf-ball::before {
+  content: "\f450"; }
+
+.fa-circle-chevron-left::before {
+  content: "\f137"; }
+
+.fa-chevron-circle-left::before {
+  content: "\f137"; }
+
+.fa-house-chimney-window::before {
+  content: "\e00d"; }
+
+.fa-pen-nib::before {
+  content: "\f5ad"; }
+
+.fa-tent-arrow-turn-left::before {
+  content: "\e580"; }
+
+.fa-tents::before {
+  content: "\e582"; }
+
+.fa-wand-magic::before {
+  content: "\f0d0"; }
+
+.fa-magic::before {
+  content: "\f0d0"; }
+
+.fa-dog::before {
+  content: "\f6d3"; }
+
+.fa-carrot::before {
+  content: "\f787"; }
+
+.fa-moon::before {
+  content: "\f186"; }
+
+.fa-wine-glass-empty::before {
+  content: "\f5ce"; }
+
+.fa-wine-glass-alt::before {
+  content: "\f5ce"; }
+
+.fa-cheese::before {
+  content: "\f7ef"; }
+
+.fa-yin-yang::before {
+  content: "\f6ad"; }
+
+.fa-music::before {
+  content: "\f001"; }
+
+.fa-code-commit::before {
+  content: "\f386"; }
+
+.fa-temperature-low::before {
+  content: "\f76b"; }
+
+.fa-person-biking::before {
+  content: "\f84a"; }
+
+.fa-biking::before {
+  content: "\f84a"; }
+
+.fa-broom::before {
+  content: "\f51a"; }
+
+.fa-shield-heart::before {
+  content: "\e574"; }
+
+.fa-gopuram::before {
+  content: "\f664"; }
+
+.fa-earth-oceania::before {
+  content: "\e47b"; }
+
+.fa-globe-oceania::before {
+  content: "\e47b"; }
+
+.fa-square-xmark::before {
+  content: "\f2d3"; }
+
+.fa-times-square::before {
+  content: "\f2d3"; }
+
+.fa-xmark-square::before {
+  content: "\f2d3"; }
+
+.fa-hashtag::before {
+  content: "\23"; }
+
+.fa-up-right-and-down-left-from-center::before {
+  content: "\f424"; }
+
+.fa-expand-alt::before {
+  content: "\f424"; }
+
+.fa-oil-can::before {
+  content: "\f613"; }
+
+.fa-t::before {
+  content: "\54"; }
+
+.fa-hippo::before {
+  content: "\f6ed"; }
+
+.fa-chart-column::before {
+  content: "\e0e3"; }
+
+.fa-infinity::before {
+  content: "\f534"; }
+
+.fa-vial-circle-check::before {
+  content: "\e596"; }
+
+.fa-person-arrow-down-to-line::before {
+  content: "\e538"; }
+
+.fa-voicemail::before {
+  content: "\f897"; }
+
+.fa-fan::before {
+  content: "\f863"; }
+
+.fa-person-walking-luggage::before {
+  content: "\e554"; }
+
+.fa-up-down::before {
+  content: "\f338"; }
+
+.fa-arrows-alt-v::before {
+  content: "\f338"; }
+
+.fa-cloud-moon-rain::before {
+  content: "\f73c"; }
+
+.fa-calendar::before {
+  content: "\f133"; }
+
+.fa-trailer::before {
+  content: "\e041"; }
+
+.fa-bahai::before {
+  content: "\f666"; }
+
+.fa-haykal::before {
+  content: "\f666"; }
+
+.fa-sd-card::before {
+  content: "\f7c2"; }
+
+.fa-dragon::before {
+  content: "\f6d5"; }
+
+.fa-shoe-prints::before {
+  content: "\f54b"; }
+
+.fa-circle-plus::before {
+  content: "\f055"; }
+
+.fa-plus-circle::before {
+  content: "\f055"; }
+
+.fa-face-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-grin-tongue-wink::before {
+  content: "\f58b"; }
+
+.fa-hand-holding::before {
+  content: "\f4bd"; }
+
+.fa-plug-circle-exclamation::before {
+  content: "\e55d"; }
+
+.fa-link-slash::before {
+  content: "\f127"; }
+
+.fa-chain-broken::before {
+  content: "\f127"; }
+
+.fa-chain-slash::before {
+  content: "\f127"; }
+
+.fa-unlink::before {
+  content: "\f127"; }
+
+.fa-clone::before {
+  content: "\f24d"; }
+
+.fa-person-walking-arrow-loop-left::before {
+  content: "\e551"; }
+
+.fa-arrow-up-z-a::before {
+  content: "\f882"; }
+
+.fa-sort-alpha-up-alt::before {
+  content: "\f882"; }
+
+.fa-fire-flame-curved::before {
+  content: "\f7e4"; }
+
+.fa-fire-alt::before {
+  content: "\f7e4"; }
+
+.fa-tornado::before {
+  content: "\f76f"; }
+
+.fa-file-circle-plus::before {
+  content: "\e494"; }
+
+.fa-book-quran::before {
+  content: "\f687"; }
+
+.fa-quran::before {
+  content: "\f687"; }
+
+.fa-anchor::before {
+  content: "\f13d"; }
+
+.fa-border-all::before {
+  content: "\f84c"; }
+
+.fa-face-angry::before {
+  content: "\f556"; }
+
+.fa-angry::before {
+  content: "\f556"; }
+
+.fa-cookie-bite::before {
+  content: "\f564"; }
+
+.fa-arrow-trend-down::before {
+  content: "\e097"; }
+
+.fa-rss::before {
+  content: "\f09e"; }
+
+.fa-feed::before {
+  content: "\f09e"; }
+
+.fa-draw-polygon::before {
+  content: "\f5ee"; }
+
+.fa-scale-balanced::before {
+  content: "\f24e"; }
+
+.fa-balance-scale::before {
+  content: "\f24e"; }
+
+.fa-gauge-simple-high::before {
+  content: "\f62a"; }
+
+.fa-tachometer::before {
+  content: "\f62a"; }
+
+.fa-tachometer-fast::before {
+  content: "\f62a"; }
+
+.fa-shower::before {
+  content: "\f2cc"; }
+
+.fa-desktop::before {
+  content: "\f390"; }
+
+.fa-desktop-alt::before {
+  content: "\f390"; }
+
+.fa-m::before {
+  content: "\4d"; }
+
+.fa-table-list::before {
+  content: "\f00b"; }
+
+.fa-th-list::before {
+  content: "\f00b"; }
+
+.fa-comment-sms::before {
+  content: "\f7cd"; }
+
+.fa-sms::before {
+  content: "\f7cd"; }
+
+.fa-book::before {
+  content: "\f02d"; }
+
+.fa-user-plus::before {
+  content: "\f234"; }
+
+.fa-check::before {
+  content: "\f00c"; }
+
+.fa-battery-three-quarters::before {
+  content: "\f241"; }
+
+.fa-battery-4::before {
+  content: "\f241"; }
+
+.fa-house-circle-check::before {
+  content: "\e509"; }
+
+.fa-angle-left::before {
+  content: "\f104"; }
+
+.fa-diagram-successor::before {
+  content: "\e47a"; }
+
+.fa-truck-arrow-right::before {
+  content: "\e58b"; }
+
+.fa-arrows-split-up-and-left::before {
+  content: "\e4bc"; }
+
+.fa-hand-fist::before {
+  content: "\f6de"; }
+
+.fa-fist-raised::before {
+  content: "\f6de"; }
+
+.fa-cloud-moon::before {
+  content: "\f6c3"; }
+
+.fa-briefcase::before {
+  content: "\f0b1"; }
+
+.fa-person-falling::before {
+  content: "\e546"; }
+
+.fa-image-portrait::before {
+  content: "\f3e0"; }
+
+.fa-portrait::before {
+  content: "\f3e0"; }
+
+.fa-user-tag::before {
+  content: "\f507"; }
+
+.fa-rug::before {
+  content: "\e569"; }
+
+.fa-earth-europe::before {
+  content: "\f7a2"; }
+
+.fa-globe-europe::before {
+  content: "\f7a2"; }
+
+.fa-cart-flatbed-suitcase::before {
+  content: "\f59d"; }
+
+.fa-luggage-cart::before {
+  content: "\f59d"; }
+
+.fa-rectangle-xmark::before {
+  content: "\f410"; }
+
+.fa-rectangle-times::before {
+  content: "\f410"; }
+
+.fa-times-rectangle::before {
+  content: "\f410"; }
+
+.fa-window-close::before {
+  content: "\f410"; }
+
+.fa-baht-sign::before {
+  content: "\e0ac"; }
+
+.fa-book-open::before {
+  content: "\f518"; }
+
+.fa-book-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-journal-whills::before {
+  content: "\f66a"; }
+
+.fa-handcuffs::before {
+  content: "\e4f8"; }
+
+.fa-triangle-exclamation::before {
+  content: "\f071"; }
+
+.fa-exclamation-triangle::before {
+  content: "\f071"; }
+
+.fa-warning::before {
+  content: "\f071"; }
+
+.fa-database::before {
+  content: "\f1c0"; }
+
+.fa-share::before {
+  content: "\f064"; }
+
+.fa-arrow-turn-right::before {
+  content: "\f064"; }
+
+.fa-mail-forward::before {
+  content: "\f064"; }
+
+.fa-bottle-droplet::before {
+  content: "\e4c4"; }
+
+.fa-mask-face::before {
+  content: "\e1d7"; }
+
+.fa-hill-rockslide::before {
+  content: "\e508"; }
+
+.fa-right-left::before {
+  content: "\f362"; }
+
+.fa-exchange-alt::before {
+  content: "\f362"; }
+
+.fa-paper-plane::before {
+  content: "\f1d8"; }
+
+.fa-road-circle-exclamation::before {
+  content: "\e565"; }
+
+.fa-dungeon::before {
+  content: "\f6d9"; }
+
+.fa-align-right::before {
+  content: "\f038"; }
+
+.fa-money-bill-1-wave::before {
+  content: "\f53b"; }
+
+.fa-money-bill-wave-alt::before {
+  content: "\f53b"; }
+
+.fa-life-ring::before {
+  content: "\f1cd"; }
+
+.fa-hands::before {
+  content: "\f2a7"; }
+
+.fa-sign-language::before {
+  content: "\f2a7"; }
+
+.fa-signing::before {
+  content: "\f2a7"; }
+
+.fa-calendar-day::before {
+  content: "\f783"; }
+
+.fa-water-ladder::before {
+  content: "\f5c5"; }
+
+.fa-ladder-water::before {
+  content: "\f5c5"; }
+
+.fa-swimming-pool::before {
+  content: "\f5c5"; }
+
+.fa-arrows-up-down::before {
+  content: "\f07d"; }
+
+.fa-arrows-v::before {
+  content: "\f07d"; }
+
+.fa-face-grimace::before {
+  content: "\f57f"; }
+
+.fa-grimace::before {
+  content: "\f57f"; }
+
+.fa-wheelchair-move::before {
+  content: "\e2ce"; }
+
+.fa-wheelchair-alt::before {
+  content: "\e2ce"; }
+
+.fa-turn-down::before {
+  content: "\f3be"; }
+
+.fa-level-down-alt::before {
+  content: "\f3be"; }
+
+.fa-person-walking-arrow-right::before {
+  content: "\e552"; }
+
+.fa-square-envelope::before {
+  content: "\f199"; }
+
+.fa-envelope-square::before {
+  content: "\f199"; }
+
+.fa-dice::before {
+  content: "\f522"; }
+
+.fa-bowling-ball::before {
+  content: "\f436"; }
+
+.fa-brain::before {
+  content: "\f5dc"; }
+
+.fa-bandage::before {
+  content: "\f462"; }
+
+.fa-band-aid::before {
+  content: "\f462"; }
+
+.fa-calendar-minus::before {
+  content: "\f272"; }
+
+.fa-circle-xmark::before {
+  content: "\f057"; }
+
+.fa-times-circle::before {
+  content: "\f057"; }
+
+.fa-xmark-circle::before {
+  content: "\f057"; }
+
+.fa-gifts::before {
+  content: "\f79c"; }
+
+.fa-hotel::before {
+  content: "\f594"; }
+
+.fa-earth-asia::before {
+  content: "\f57e"; }
+
+.fa-globe-asia::before {
+  content: "\f57e"; }
+
+.fa-id-card-clip::before {
+  content: "\f47f"; }
+
+.fa-id-card-alt::before {
+  content: "\f47f"; }
+
+.fa-magnifying-glass-plus::before {
+  content: "\f00e"; }
+
+.fa-search-plus::before {
+  content: "\f00e"; }
+
+.fa-thumbs-up::before {
+  content: "\f164"; }
+
+.fa-user-clock::before {
+  content: "\f4fd"; }
+
+.fa-hand-dots::before {
+  content: "\f461"; }
+
+.fa-allergies::before {
+  content: "\f461"; }
+
+.fa-file-invoice::before {
+  content: "\f570"; }
+
+.fa-window-minimize::before {
+  content: "\f2d1"; }
+
+.fa-mug-saucer::before {
+  content: "\f0f4"; }
+
+.fa-coffee::before {
+  content: "\f0f4"; }
+
+.fa-brush::before {
+  content: "\f55d"; }
+
+.fa-mask::before {
+  content: "\f6fa"; }
+
+.fa-magnifying-glass-minus::before {
+  content: "\f010"; }
+
+.fa-search-minus::before {
+  content: "\f010"; }
+
+.fa-ruler-vertical::before {
+  content: "\f548"; }
+
+.fa-user-large::before {
+  content: "\f406"; }
+
+.fa-user-alt::before {
+  content: "\f406"; }
+
+.fa-train-tram::before {
+  content: "\e5b4"; }
+
+.fa-user-nurse::before {
+  content: "\f82f"; }
+
+.fa-syringe::before {
+  content: "\f48e"; }
+
+.fa-cloud-sun::before {
+  content: "\f6c4"; }
+
+.fa-stopwatch-20::before {
+  content: "\e06f"; }
+
+.fa-square-full::before {
+  content: "\f45c"; }
+
+.fa-magnet::before {
+  content: "\f076"; }
+
+.fa-jar::before {
+  content: "\e516"; }
+
+.fa-note-sticky::before {
+  content: "\f249"; }
+
+.fa-sticky-note::before {
+  content: "\f249"; }
+
+.fa-bug-slash::before {
+  content: "\e490"; }
+
+.fa-arrow-up-from-water-pump::before {
+  content: "\e4b6"; }
+
+.fa-bone::before {
+  content: "\f5d7"; }
+
+.fa-user-injured::before {
+  content: "\f728"; }
+
+.fa-face-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-sad-tear::before {
+  content: "\f5b4"; }
+
+.fa-plane::before {
+  content: "\f072"; }
+
+.fa-tent-arrows-down::before {
+  content: "\e581"; }
+
+.fa-exclamation::before {
+  content: "\21"; }
+
+.fa-arrows-spin::before {
+  content: "\e4bb"; }
+
+.fa-print::before {
+  content: "\f02f"; }
+
+.fa-turkish-lira-sign::before {
+  content: "\e2bb"; }
+
+.fa-try::before {
+  content: "\e2bb"; }
+
+.fa-turkish-lira::before {
+  content: "\e2bb"; }
+
+.fa-dollar-sign::before {
+  content: "\24"; }
+
+.fa-dollar::before {
+  content: "\24"; }
+
+.fa-usd::before {
+  content: "\24"; }
+
+.fa-x::before {
+  content: "\58"; }
+
+.fa-magnifying-glass-dollar::before {
+  content: "\f688"; }
+
+.fa-search-dollar::before {
+  content: "\f688"; }
+
+.fa-users-gear::before {
+  content: "\f509"; }
+
+.fa-users-cog::before {
+  content: "\f509"; }
+
+.fa-person-military-pointing::before {
+  content: "\e54a"; }
+
+.fa-building-columns::before {
+  content: "\f19c"; }
+
+.fa-bank::before {
+  content: "\f19c"; }
+
+.fa-institution::before {
+  content: "\f19c"; }
+
+.fa-museum::before {
+  content: "\f19c"; }
+
+.fa-university::before {
+  content: "\f19c"; }
+
+.fa-umbrella::before {
+  content: "\f0e9"; }
+
+.fa-trowel::before {
+  content: "\e589"; }
+
+.fa-d::before {
+  content: "\44"; }
+
+.fa-stapler::before {
+  content: "\e5af"; }
+
+.fa-masks-theater::before {
+  content: "\f630"; }
+
+.fa-theater-masks::before {
+  content: "\f630"; }
+
+.fa-kip-sign::before {
+  content: "\e1c4"; }
+
+.fa-hand-point-left::before {
+  content: "\f0a5"; }
+
+.fa-handshake-simple::before {
+  content: "\f4c6"; }
+
+.fa-handshake-alt::before {
+  content: "\f4c6"; }
+
+.fa-jet-fighter::before {
+  content: "\f0fb"; }
+
+.fa-fighter-jet::before {
+  content: "\f0fb"; }
+
+.fa-square-share-nodes::before {
+  content: "\f1e1"; }
+
+.fa-share-alt-square::before {
+  content: "\f1e1"; }
+
+.fa-barcode::before {
+  content: "\f02a"; }
+
+.fa-plus-minus::before {
+  content: "\e43c"; }
+
+.fa-video::before {
+  content: "\f03d"; }
+
+.fa-video-camera::before {
+  content: "\f03d"; }
+
+.fa-graduation-cap::before {
+  content: "\f19d"; }
+
+.fa-mortar-board::before {
+  content: "\f19d"; }
+
+.fa-hand-holding-medical::before {
+  content: "\e05c"; }
+
+.fa-person-circle-check::before {
+  content: "\e53e"; }
+
+.fa-turn-up::before {
+  content: "\f3bf"; }
+
+.fa-level-up-alt::before {
+  content: "\f3bf"; }
+
+.sr-only,
+.fa-sr-only {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+
+.sr-only-focusable:not(:focus),
+.fa-sr-only-focusable:not(:focus) {
+  position: absolute;
+  width: 1px;
+  height: 1px;
+  padding: 0;
+  margin: -1px;
+  overflow: hidden;
+  clip: rect(0, 0, 0, 0);
+  white-space: nowrap;
+  border-width: 0; }
+:root, :host {
+  --fa-style-family-brands: 'Font Awesome 6 Brands';
+  --fa-font-brands: normal 400 1em/1 'Font Awesome 6 Brands'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Brands';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+.fab,
+.fa-brands {
+  font-weight: 400; }
+
+.fa-monero:before {
+  content: "\f3d0"; }
+
+.fa-hooli:before {
+  content: "\f427"; }
+
+.fa-yelp:before {
+  content: "\f1e9"; }
+
+.fa-cc-visa:before {
+  content: "\f1f0"; }
+
+.fa-lastfm:before {
+  content: "\f202"; }
+
+.fa-shopware:before {
+  content: "\f5b5"; }
+
+.fa-creative-commons-nc:before {
+  content: "\f4e8"; }
+
+.fa-aws:before {
+  content: "\f375"; }
+
+.fa-redhat:before {
+  content: "\f7bc"; }
+
+.fa-yoast:before {
+  content: "\f2b1"; }
+
+.fa-cloudflare:before {
+  content: "\e07d"; }
+
+.fa-ups:before {
+  content: "\f7e0"; }
+
+.fa-wpexplorer:before {
+  content: "\f2de"; }
+
+.fa-dyalog:before {
+  content: "\f399"; }
+
+.fa-bity:before {
+  content: "\f37a"; }
+
+.fa-stackpath:before {
+  content: "\f842"; }
+
+.fa-buysellads:before {
+  content: "\f20d"; }
+
+.fa-first-order:before {
+  content: "\f2b0"; }
+
+.fa-modx:before {
+  content: "\f285"; }
+
+.fa-guilded:before {
+  content: "\e07e"; }
+
+.fa-vnv:before {
+  content: "\f40b"; }
+
+.fa-square-js:before {
+  content: "\f3b9"; }
+
+.fa-js-square:before {
+  content: "\f3b9"; }
+
+.fa-microsoft:before {
+  content: "\f3ca"; }
+
+.fa-qq:before {
+  content: "\f1d6"; }
+
+.fa-orcid:before {
+  content: "\f8d2"; }
+
+.fa-java:before {
+  content: "\f4e4"; }
+
+.fa-invision:before {
+  content: "\f7b0"; }
+
+.fa-creative-commons-pd-alt:before {
+  content: "\f4ed"; }
+
+.fa-centercode:before {
+  content: "\f380"; }
+
+.fa-glide-g:before {
+  content: "\f2a6"; }
+
+.fa-drupal:before {
+  content: "\f1a9"; }
+
+.fa-hire-a-helper:before {
+  content: "\f3b0"; }
+
+.fa-creative-commons-by:before {
+  content: "\f4e7"; }
+
+.fa-unity:before {
+  content: "\e049"; }
+
+.fa-whmcs:before {
+  content: "\f40d"; }
+
+.fa-rocketchat:before {
+  content: "\f3e8"; }
+
+.fa-vk:before {
+  content: "\f189"; }
+
+.fa-untappd:before {
+  content: "\f405"; }
+
+.fa-mailchimp:before {
+  content: "\f59e"; }
+
+.fa-css3-alt:before {
+  content: "\f38b"; }
+
+.fa-square-reddit:before {
+  content: "\f1a2"; }
+
+.fa-reddit-square:before {
+  content: "\f1a2"; }
+
+.fa-vimeo-v:before {
+  content: "\f27d"; }
+
+.fa-contao:before {
+  content: "\f26d"; }
+
+.fa-square-font-awesome:before {
+  content: "\e5ad"; }
+
+.fa-deskpro:before {
+  content: "\f38f"; }
+
+.fa-sistrix:before {
+  content: "\f3ee"; }
+
+.fa-square-instagram:before {
+  content: "\e055"; }
+
+.fa-instagram-square:before {
+  content: "\e055"; }
+
+.fa-battle-net:before {
+  content: "\f835"; }
+
+.fa-the-red-yeti:before {
+  content: "\f69d"; }
+
+.fa-square-hacker-news:before {
+  content: "\f3af"; }
+
+.fa-hacker-news-square:before {
+  content: "\f3af"; }
+
+.fa-edge:before {
+  content: "\f282"; }
+
+.fa-threads:before {
+  content: "\e618"; }
+
+.fa-napster:before {
+  content: "\f3d2"; }
+
+.fa-square-snapchat:before {
+  content: "\f2ad"; }
+
+.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa-google-plus-g:before {
+  content: "\f0d5"; }
+
+.fa-artstation:before {
+  content: "\f77a"; }
+
+.fa-markdown:before {
+  content: "\f60f"; }
+
+.fa-sourcetree:before {
+  content: "\f7d3"; }
+
+.fa-google-plus:before {
+  content: "\f2b3"; }
+
+.fa-diaspora:before {
+  content: "\f791"; }
+
+.fa-foursquare:before {
+  content: "\f180"; }
+
+.fa-stack-overflow:before {
+  content: "\f16c"; }
+
+.fa-github-alt:before {
+  content: "\f113"; }
+
+.fa-phoenix-squadron:before {
+  content: "\f511"; }
+
+.fa-pagelines:before {
+  content: "\f18c"; }
+
+.fa-algolia:before {
+  content: "\f36c"; }
+
+.fa-red-river:before {
+  content: "\f3e3"; }
+
+.fa-creative-commons-sa:before {
+  content: "\f4ef"; }
+
+.fa-safari:before {
+  content: "\f267"; }
+
+.fa-google:before {
+  content: "\f1a0"; }
+
+.fa-square-font-awesome-stroke:before {
+  content: "\f35c"; }
+
+.fa-font-awesome-alt:before {
+  content: "\f35c"; }
+
+.fa-atlassian:before {
+  content: "\f77b"; }
+
+.fa-linkedin-in:before {
+  content: "\f0e1"; }
+
+.fa-digital-ocean:before {
+  content: "\f391"; }
+
+.fa-nimblr:before {
+  content: "\f5a8"; }
+
+.fa-chromecast:before {
+  content: "\f838"; }
+
+.fa-evernote:before {
+  content: "\f839"; }
+
+.fa-hacker-news:before {
+  content: "\f1d4"; }
+
+.fa-creative-commons-sampling:before {
+  content: "\f4f0"; }
+
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+  content: "\f5cf"; }
+
+.fa-square-behance:before {
+  content: "\f1b5"; }
+
+.fa-behance-square:before {
+  content: "\f1b5"; }
+
+.fa-supple:before {
+  content: "\f3f9"; }
+
+.fa-rebel:before {
+  content: "\f1d0"; }
+
+.fa-css3:before {
+  content: "\f13c"; }
+
+.fa-staylinked:before {
+  content: "\f3f5"; }
+
+.fa-kaggle:before {
+  content: "\f5fa"; }
+
+.fa-space-awesome:before {
+  content: "\e5ac"; }
+
+.fa-deviantart:before {
+  content: "\f1bd"; }
+
+.fa-cpanel:before {
+  content: "\f388"; }
+
+.fa-goodreads-g:before {
+  content: "\f3a9"; }
+
+.fa-square-git:before {
+  content: "\f1d2"; }
+
+.fa-git-square:before {
+  content: "\f1d2"; }
+
+.fa-square-tumblr:before {
+  content: "\f174"; }
+
+.fa-tumblr-square:before {
+  content: "\f174"; }
+
+.fa-trello:before {
+  content: "\f181"; }
+
+.fa-creative-commons-nc-jp:before {
+  content: "\f4ea"; }
+
+.fa-get-pocket:before {
+  content: "\f265"; }
+
+.fa-perbyte:before {
+  content: "\e083"; }
+
+.fa-grunt:before {
+  content: "\f3ad"; }
+
+.fa-weebly:before {
+  content: "\f5cc"; }
+
+.fa-connectdevelop:before {
+  content: "\f20e"; }
+
+.fa-leanpub:before {
+  content: "\f212"; }
+
+.fa-black-tie:before {
+  content: "\f27e"; }
+
+.fa-themeco:before {
+  content: "\f5c6"; }
+
+.fa-python:before {
+  content: "\f3e2"; }
+
+.fa-android:before {
+  content: "\f17b"; }
+
+.fa-bots:before {
+  content: "\e340"; }
+
+.fa-free-code-camp:before {
+  content: "\f2c5"; }
+
+.fa-hornbill:before {
+  content: "\f592"; }
+
+.fa-js:before {
+  content: "\f3b8"; }
+
+.fa-ideal:before {
+  content: "\e013"; }
+
+.fa-git:before {
+  content: "\f1d3"; }
+
+.fa-dev:before {
+  content: "\f6cc"; }
+
+.fa-sketch:before {
+  content: "\f7c6"; }
+
+.fa-yandex-international:before {
+  content: "\f414"; }
+
+.fa-cc-amex:before {
+  content: "\f1f3"; }
+
+.fa-uber:before {
+  content: "\f402"; }
+
+.fa-github:before {
+  content: "\f09b"; }
+
+.fa-php:before {
+  content: "\f457"; }
+
+.fa-alipay:before {
+  content: "\f642"; }
+
+.fa-youtube:before {
+  content: "\f167"; }
+
+.fa-skyatlas:before {
+  content: "\f216"; }
+
+.fa-firefox-browser:before {
+  content: "\e007"; }
+
+.fa-replyd:before {
+  content: "\f3e6"; }
+
+.fa-suse:before {
+  content: "\f7d6"; }
+
+.fa-jenkins:before {
+  content: "\f3b6"; }
+
+.fa-twitter:before {
+  content: "\f099"; }
+
+.fa-rockrms:before {
+  content: "\f3e9"; }
+
+.fa-pinterest:before {
+  content: "\f0d2"; }
+
+.fa-buffer:before {
+  content: "\f837"; }
+
+.fa-npm:before {
+  content: "\f3d4"; }
+
+.fa-yammer:before {
+  content: "\f840"; }
+
+.fa-btc:before {
+  content: "\f15a"; }
+
+.fa-dribbble:before {
+  content: "\f17d"; }
+
+.fa-stumbleupon-circle:before {
+  content: "\f1a3"; }
+
+.fa-internet-explorer:before {
+  content: "\f26b"; }
+
+.fa-stubber:before {
+  content: "\e5c7"; }
+
+.fa-telegram:before {
+  content: "\f2c6"; }
+
+.fa-telegram-plane:before {
+  content: "\f2c6"; }
+
+.fa-old-republic:before {
+  content: "\f510"; }
+
+.fa-odysee:before {
+  content: "\e5c6"; }
+
+.fa-square-whatsapp:before {
+  content: "\f40c"; }
+
+.fa-whatsapp-square:before {
+  content: "\f40c"; }
+
+.fa-node-js:before {
+  content: "\f3d3"; }
+
+.fa-edge-legacy:before {
+  content: "\e078"; }
+
+.fa-slack:before {
+  content: "\f198"; }
+
+.fa-slack-hash:before {
+  content: "\f198"; }
+
+.fa-medrt:before {
+  content: "\f3c8"; }
+
+.fa-usb:before {
+  content: "\f287"; }
+
+.fa-tumblr:before {
+  content: "\f173"; }
+
+.fa-vaadin:before {
+  content: "\f408"; }
+
+.fa-quora:before {
+  content: "\f2c4"; }
+
+.fa-square-x-twitter:before {
+  content: "\e61a"; }
+
+.fa-reacteurope:before {
+  content: "\f75d"; }
+
+.fa-medium:before {
+  content: "\f23a"; }
+
+.fa-medium-m:before {
+  content: "\f23a"; }
+
+.fa-amilia:before {
+  content: "\f36d"; }
+
+.fa-mixcloud:before {
+  content: "\f289"; }
+
+.fa-flipboard:before {
+  content: "\f44d"; }
+
+.fa-viacoin:before {
+  content: "\f237"; }
+
+.fa-critical-role:before {
+  content: "\f6c9"; }
+
+.fa-sitrox:before {
+  content: "\e44a"; }
+
+.fa-discourse:before {
+  content: "\f393"; }
+
+.fa-joomla:before {
+  content: "\f1aa"; }
+
+.fa-mastodon:before {
+  content: "\f4f6"; }
+
+.fa-airbnb:before {
+  content: "\f834"; }
+
+.fa-wolf-pack-battalion:before {
+  content: "\f514"; }
+
+.fa-buy-n-large:before {
+  content: "\f8a6"; }
+
+.fa-gulp:before {
+  content: "\f3ae"; }
+
+.fa-creative-commons-sampling-plus:before {
+  content: "\f4f1"; }
+
+.fa-strava:before {
+  content: "\f428"; }
+
+.fa-ember:before {
+  content: "\f423"; }
+
+.fa-canadian-maple-leaf:before {
+  content: "\f785"; }
+
+.fa-teamspeak:before {
+  content: "\f4f9"; }
+
+.fa-pushed:before {
+  content: "\f3e1"; }
+
+.fa-wordpress-simple:before {
+  content: "\f411"; }
+
+.fa-nutritionix:before {
+  content: "\f3d6"; }
+
+.fa-wodu:before {
+  content: "\e088"; }
+
+.fa-google-pay:before {
+  content: "\e079"; }
+
+.fa-intercom:before {
+  content: "\f7af"; }
+
+.fa-zhihu:before {
+  content: "\f63f"; }
+
+.fa-korvue:before {
+  content: "\f42f"; }
+
+.fa-pix:before {
+  content: "\e43a"; }
+
+.fa-steam-symbol:before {
+  content: "\f3f6"; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-regular: normal 400 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 400;
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+.far,
+.fa-regular {
+  font-weight: 400; }
+:root, :host {
+  --fa-style-family-classic: 'Font Awesome 6 Free';
+  --fa-font-solid: normal 900 1em/1 'Font Awesome 6 Free'; }
+
+@font-face {
+  font-family: 'Font Awesome 6 Free';
+  font-style: normal;
+  font-weight: 900;
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+.fas,
+.fa-solid {
+  font-weight: 900; }
+@font-face {
+  font-family: 'Font Awesome 5 Brands';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 900;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'Font Awesome 5 Free';
+  font-display: block;
+  font-weight: 400;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-solid-900.woff2") format("woff2"), url("../webfonts/fa-solid-900.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-brands-400.woff2") format("woff2"), url("../webfonts/fa-brands-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-regular-400.woff2") format("woff2"), url("../webfonts/fa-regular-400.ttf") format("truetype"); }
+
+@font-face {
+  font-family: 'FontAwesome';
+  font-display: block;
+  src: url("../webfonts/fa-v4compatibility.woff2") format("woff2"), url("../webfonts/fa-v4compatibility.ttf") format("truetype"); }
diff --git a/deps/font-awesome-6.4.2/css/all.min.css b/deps/font-awesome-6.4.2/css/all.min.css
new file mode 100644
index 0000000..6604a06
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/all.min.css
@@ -0,0 +1,9 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa{font-family:var(--fa-style-family,"Font Awesome 6 Free");font-weight:var(--fa-style,900)}.fa,.fa-brands,.fa-classic,.fa-regular,.fa-sharp,.fa-solid,.fab,.far,.fas{-moz-osx-font-smoothing:grayscale;-webkit-font-smoothing:antialiased;display:var(--fa-display,inline-block);font-style:normal;font-variant:normal;line-height:1;text-rendering:auto}.fa-classic,.fa-regular,.fa-solid,.far,.fas{font-family:"Font Awesome 6 Free"}.fa-brands,.fab{font-family:"Font Awesome 6 Brands"}.fa-1x{font-size:1em}.fa-2x{font-size:2em}.fa-3x{font-size:3em}.fa-4x{font-size:4em}.fa-5x{font-size:5em}.fa-6x{font-size:6em}.fa-7x{font-size:7em}.fa-8x{font-size:8em}.fa-9x{font-size:9em}.fa-10x{font-size:10em}.fa-2xs{font-size:.625em;line-height:.1em;vertical-align:.225em}.fa-xs{font-size:.75em;line-height:.08333em;vertical-align:.125em}.fa-sm{font-size:.875em;line-height:.07143em;vertical-align:.05357em}.fa-lg{font-size:1.25em;line-height:.05em;vertical-align:-.075em}.fa-xl{font-size:1.5em;line-height:.04167em;vertical-align:-.125em}.fa-2xl{font-size:2em;line-height:.03125em;vertical-align:-.1875em}.fa-fw{text-align:center;width:1.25em}.fa-ul{list-style-type:none;margin-left:var(--fa-li-margin,2.5em);padding-left:0}.fa-ul>li{position:relative}.fa-li{left:calc(var(--fa-li-width, 2em)*-1);position:absolute;text-align:center;width:var(--fa-li-width,2em);line-height:inherit}.fa-border{border-radius:var(--fa-border-radius,.1em);border:var(--fa-border-width,.08em) var(--fa-border-style,solid) var(--fa-border-color,#eee);padding:var(--fa-border-padding,.2em .25em .15em)}.fa-pull-left{float:left;margin-right:var(--fa-pull-margin,.3em)}.fa-pull-right{float:right;margin-left:var(--fa-pull-margin,.3em)}.fa-beat{-webkit-animation-name:fa-beat;animation-name:fa-beat;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,ease-in-out);animation-timing-function:var(--fa-animation-timing,ease-in-out)}.fa-bounce{-webkit-animation-name:fa-bounce;animation-name:fa-bounce;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.28,.84,.42,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.28,.84,.42,1))}.fa-fade{-webkit-animation-name:fa-fade;animation-name:fa-fade;-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1))}.fa-beat-fade,.fa-fade{-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s)}.fa-beat-fade{-webkit-animation-name:fa-beat-fade;animation-name:fa-beat-fade;-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1));animation-timing-function:var(--fa-animation-timing,cubic-bezier(.4,0,.6,1))}.fa-flip{-webkit-animation-name:fa-flip;animation-name:fa-flip;-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,ease-in-out);animation-timing-function:var(--fa-animation-timing,ease-in-out)}.fa-shake{-webkit-animation-name:fa-shake;animation-name:fa-shake;-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,linear);animation-timing-function:var(--fa-animation-timing,linear)}.fa-shake,.fa-spin{-webkit-animation-delay:var(--fa-animation-delay,0s);animation-delay:var(--fa-animation-delay,0s);-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal)}.fa-spin{-webkit-animation-name:fa-spin;animation-name:fa-spin;-webkit-animation-duration:var(--fa-animation-duration,2s);animation-duration:var(--fa-animation-duration,2s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,linear);animation-timing-function:var(--fa-animation-timing,linear)}.fa-spin-reverse{--fa-animation-direction:reverse}.fa-pulse,.fa-spin-pulse{-webkit-animation-name:fa-spin;animation-name:fa-spin;-webkit-animation-direction:var(--fa-animation-direction,normal);animation-direction:var(--fa-animation-direction,normal);-webkit-animation-duration:var(--fa-animation-duration,1s);animation-duration:var(--fa-animation-duration,1s);-webkit-animation-iteration-count:var(--fa-animation-iteration-count,infinite);animation-iteration-count:var(--fa-animation-iteration-count,infinite);-webkit-animation-timing-function:var(--fa-animation-timing,steps(8));animation-timing-function:var(--fa-animation-timing,steps(8))}@media (prefers-reduced-motion:reduce){.fa-beat,.fa-beat-fade,.fa-bounce,.fa-fade,.fa-flip,.fa-pulse,.fa-shake,.fa-spin,.fa-spin-pulse{-webkit-animation-delay:-1ms;animation-delay:-1ms;-webkit-animation-duration:1ms;animation-duration:1ms;-webkit-animation-iteration-count:1;animation-iteration-count:1;-webkit-transition-delay:0s;transition-delay:0s;-webkit-transition-duration:0s;transition-duration:0s}}@-webkit-keyframes fa-beat{0%,90%{-webkit-transform:scale(1);transform:scale(1)}45%{-webkit-transform:scale(var(--fa-beat-scale,1.25));transform:scale(var(--fa-beat-scale,1.25))}}@keyframes fa-beat{0%,90%{-webkit-transform:scale(1);transform:scale(1)}45%{-webkit-transform:scale(var(--fa-beat-scale,1.25));transform:scale(var(--fa-beat-scale,1.25))}}@-webkit-keyframes fa-bounce{0%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}}@keyframes fa-bounce{0%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}10%{-webkit-transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0);transform:scale(var(--fa-bounce-start-scale-x,1.1),var(--fa-bounce-start-scale-y,.9)) translateY(0)}30%{-webkit-transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em));transform:scale(var(--fa-bounce-jump-scale-x,.9),var(--fa-bounce-jump-scale-y,1.1)) translateY(var(--fa-bounce-height,-.5em))}50%{-webkit-transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0);transform:scale(var(--fa-bounce-land-scale-x,1.05),var(--fa-bounce-land-scale-y,.95)) translateY(0)}57%{-webkit-transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em));transform:scale(1) translateY(var(--fa-bounce-rebound,-.125em))}64%{-webkit-transform:scale(1) translateY(0);transform:scale(1) translateY(0)}to{-webkit-transform:scale(1) translateY(0);transform:scale(1) 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\ No newline at end of file
diff --git a/deps/font-awesome-6.4.2/css/v4-shims.css b/deps/font-awesome-6.4.2/css/v4-shims.css
new file mode 100644
index 0000000..a85953d
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/v4-shims.css
@@ -0,0 +1,2194 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
+.fa.fa-glass:before {
+  content: "\f000"; }
+
+.fa.fa-envelope-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-o:before {
+  content: "\f0e0"; }
+
+.fa.fa-star-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-o:before {
+  content: "\f005"; }
+
+.fa.fa-remove:before {
+  content: "\f00d"; }
+
+.fa.fa-close:before {
+  content: "\f00d"; }
+
+.fa.fa-gear:before {
+  content: "\f013"; }
+
+.fa.fa-trash-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-trash-o:before {
+  content: "\f2ed"; }
+
+.fa.fa-home:before {
+  content: "\f015"; }
+
+.fa.fa-file-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-file-o:before {
+  content: "\f15b"; }
+
+.fa.fa-clock-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-clock-o:before {
+  content: "\f017"; }
+
+.fa.fa-arrow-circle-o-down {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-arrow-circle-o-down:before {
+  content: "\f358"; }
+
+.fa.fa-arrow-circle-o-up {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-arrow-circle-o-up:before {
+  content: "\f35b"; }
+
+.fa.fa-play-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-play-circle-o:before {
+  content: "\f144"; }
+
+.fa.fa-repeat:before {
+  content: "\f01e"; }
+
+.fa.fa-rotate-right:before {
+  content: "\f01e"; }
+
+.fa.fa-refresh:before {
+  content: "\f021"; }
+
+.fa.fa-list-alt {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-list-alt:before {
+  content: "\f022"; }
+
+.fa.fa-dedent:before {
+  content: "\f03b"; }
+
+.fa.fa-video-camera:before {
+  content: "\f03d"; }
+
+.fa.fa-picture-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-picture-o:before {
+  content: "\f03e"; }
+
+.fa.fa-photo {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-photo:before {
+  content: "\f03e"; }
+
+.fa.fa-image {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-image:before {
+  content: "\f03e"; }
+
+.fa.fa-map-marker:before {
+  content: "\f3c5"; }
+
+.fa.fa-pencil-square-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-pencil-square-o:before {
+  content: "\f044"; }
+
+.fa.fa-edit {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-edit:before {
+  content: "\f044"; }
+
+.fa.fa-share-square-o:before {
+  content: "\f14d"; }
+
+.fa.fa-check-square-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-check-square-o:before {
+  content: "\f14a"; }
+
+.fa.fa-arrows:before {
+  content: "\f0b2"; }
+
+.fa.fa-times-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-circle-o:before {
+  content: "\f057"; }
+
+.fa.fa-check-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-check-circle-o:before {
+  content: "\f058"; }
+
+.fa.fa-mail-forward:before {
+  content: "\f064"; }
+
+.fa.fa-expand:before {
+  content: "\f424"; }
+
+.fa.fa-compress:before {
+  content: "\f422"; }
+
+.fa.fa-eye {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-eye-slash {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-warning:before {
+  content: "\f071"; }
+
+.fa.fa-calendar:before {
+  content: "\f073"; }
+
+.fa.fa-arrows-v:before {
+  content: "\f338"; }
+
+.fa.fa-arrows-h:before {
+  content: "\f337"; }
+
+.fa.fa-bar-chart:before {
+  content: "\e0e3"; }
+
+.fa.fa-bar-chart-o:before {
+  content: "\e0e3"; }
+
+.fa.fa-twitter-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-twitter-square:before {
+  content: "\f081"; }
+
+.fa.fa-facebook-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-facebook-square:before {
+  content: "\f082"; }
+
+.fa.fa-gears:before {
+  content: "\f085"; }
+
+.fa.fa-thumbs-o-up {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-thumbs-o-up:before {
+  content: "\f164"; }
+
+.fa.fa-thumbs-o-down {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-thumbs-o-down:before {
+  content: "\f165"; }
+
+.fa.fa-heart-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-heart-o:before {
+  content: "\f004"; }
+
+.fa.fa-sign-out:before {
+  content: "\f2f5"; }
+
+.fa.fa-linkedin-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-linkedin-square:before {
+  content: "\f08c"; }
+
+.fa.fa-thumb-tack:before {
+  content: "\f08d"; }
+
+.fa.fa-external-link:before {
+  content: "\f35d"; }
+
+.fa.fa-sign-in:before {
+  content: "\f2f6"; }
+
+.fa.fa-github-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-github-square:before {
+  content: "\f092"; }
+
+.fa.fa-lemon-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-lemon-o:before {
+  content: "\f094"; }
+
+.fa.fa-square-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-square-o:before {
+  content: "\f0c8"; }
+
+.fa.fa-bookmark-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-bookmark-o:before {
+  content: "\f02e"; }
+
+.fa.fa-twitter {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-facebook {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-facebook:before {
+  content: "\f39e"; }
+
+.fa.fa-facebook-f {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-facebook-f:before {
+  content: "\f39e"; }
+
+.fa.fa-github {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-credit-card {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-feed:before {
+  content: "\f09e"; }
+
+.fa.fa-hdd-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hdd-o:before {
+  content: "\f0a0"; }
+
+.fa.fa-hand-o-right {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-o-right:before {
+  content: "\f0a4"; }
+
+.fa.fa-hand-o-left {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-o-left:before {
+  content: "\f0a5"; }
+
+.fa.fa-hand-o-up {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-o-up:before {
+  content: "\f0a6"; }
+
+.fa.fa-hand-o-down {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-o-down:before {
+  content: "\f0a7"; }
+
+.fa.fa-globe:before {
+  content: "\f57d"; }
+
+.fa.fa-tasks:before {
+  content: "\f828"; }
+
+.fa.fa-arrows-alt:before {
+  content: "\f31e"; }
+
+.fa.fa-group:before {
+  content: "\f0c0"; }
+
+.fa.fa-chain:before {
+  content: "\f0c1"; }
+
+.fa.fa-cut:before {
+  content: "\f0c4"; }
+
+.fa.fa-files-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-files-o:before {
+  content: "\f0c5"; }
+
+.fa.fa-floppy-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-floppy-o:before {
+  content: "\f0c7"; }
+
+.fa.fa-save {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-save:before {
+  content: "\f0c7"; }
+
+.fa.fa-navicon:before {
+  content: "\f0c9"; }
+
+.fa.fa-reorder:before {
+  content: "\f0c9"; }
+
+.fa.fa-magic:before {
+  content: "\e2ca"; }
+
+.fa.fa-pinterest {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-pinterest-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-pinterest-square:before {
+  content: "\f0d3"; }
+
+.fa.fa-google-plus-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-square:before {
+  content: "\f0d4"; }
+
+.fa.fa-google-plus {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus:before {
+  content: "\f0d5"; }
+
+.fa.fa-money:before {
+  content: "\f3d1"; }
+
+.fa.fa-unsorted:before {
+  content: "\f0dc"; }
+
+.fa.fa-sort-desc:before {
+  content: "\f0dd"; }
+
+.fa.fa-sort-asc:before {
+  content: "\f0de"; }
+
+.fa.fa-linkedin {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-linkedin:before {
+  content: "\f0e1"; }
+
+.fa.fa-rotate-left:before {
+  content: "\f0e2"; }
+
+.fa.fa-legal:before {
+  content: "\f0e3"; }
+
+.fa.fa-tachometer:before {
+  content: "\f625"; }
+
+.fa.fa-dashboard:before {
+  content: "\f625"; }
+
+.fa.fa-comment-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-comment-o:before {
+  content: "\f075"; }
+
+.fa.fa-comments-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-comments-o:before {
+  content: "\f086"; }
+
+.fa.fa-flash:before {
+  content: "\f0e7"; }
+
+.fa.fa-clipboard:before {
+  content: "\f0ea"; }
+
+.fa.fa-lightbulb-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-lightbulb-o:before {
+  content: "\f0eb"; }
+
+.fa.fa-exchange:before {
+  content: "\f362"; }
+
+.fa.fa-cloud-download:before {
+  content: "\f0ed"; }
+
+.fa.fa-cloud-upload:before {
+  content: "\f0ee"; }
+
+.fa.fa-bell-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-bell-o:before {
+  content: "\f0f3"; }
+
+.fa.fa-cutlery:before {
+  content: "\f2e7"; }
+
+.fa.fa-file-text-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-file-text-o:before {
+  content: "\f15c"; }
+
+.fa.fa-building-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-building-o:before {
+  content: "\f1ad"; }
+
+.fa.fa-hospital-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hospital-o:before {
+  content: "\f0f8"; }
+
+.fa.fa-tablet:before {
+  content: "\f3fa"; }
+
+.fa.fa-mobile:before {
+  content: "\f3cd"; }
+
+.fa.fa-mobile-phone:before {
+  content: "\f3cd"; }
+
+.fa.fa-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-circle-o:before {
+  content: "\f111"; }
+
+.fa.fa-mail-reply:before {
+  content: "\f3e5"; }
+
+.fa.fa-github-alt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-folder-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-folder-o:before {
+  content: "\f07b"; }
+
+.fa.fa-folder-open-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-folder-open-o:before {
+  content: "\f07c"; }
+
+.fa.fa-smile-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-smile-o:before {
+  content: "\f118"; }
+
+.fa.fa-frown-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-frown-o:before {
+  content: "\f119"; }
+
+.fa.fa-meh-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-meh-o:before {
+  content: "\f11a"; }
+
+.fa.fa-keyboard-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-keyboard-o:before {
+  content: "\f11c"; }
+
+.fa.fa-flag-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-flag-o:before {
+  content: "\f024"; }
+
+.fa.fa-mail-reply-all:before {
+  content: "\f122"; }
+
+.fa.fa-star-half-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-half-o:before {
+  content: "\f5c0"; }
+
+.fa.fa-star-half-empty {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-half-empty:before {
+  content: "\f5c0"; }
+
+.fa.fa-star-half-full {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-star-half-full:before {
+  content: "\f5c0"; }
+
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+  content: "\f203"; }
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+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
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+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-cc {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-cc:before {
+  content: "\f20a"; }
+
+.fa.fa-ils:before {
+  content: "\f20b"; }
+
+.fa.fa-shekel:before {
+  content: "\f20b"; }
+
+.fa.fa-sheqel:before {
+  content: "\f20b"; }
+
+.fa.fa-buysellads {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-connectdevelop {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-dashcube {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-forumbee {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-leanpub {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-sellsy {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-shirtsinbulk {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-simplybuilt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-skyatlas {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-diamond {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-diamond:before {
+  content: "\f3a5"; }
+
+.fa.fa-transgender:before {
+  content: "\f224"; }
+
+.fa.fa-intersex:before {
+  content: "\f224"; }
+
+.fa.fa-transgender-alt:before {
+  content: "\f225"; }
+
+.fa.fa-facebook-official {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
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+  content: "\f09a"; }
+
+.fa.fa-pinterest-p {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-whatsapp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-hotel:before {
+  content: "\f236"; }
+
+.fa.fa-viacoin {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-medium {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-y-combinator {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-yc {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-yc:before {
+  content: "\f23b"; }
+
+.fa.fa-optin-monster {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-opencart {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-expeditedssl {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-battery-4:before {
+  content: "\f240"; }
+
+.fa.fa-battery:before {
+  content: "\f240"; }
+
+.fa.fa-battery-3:before {
+  content: "\f241"; }
+
+.fa.fa-battery-2:before {
+  content: "\f242"; }
+
+.fa.fa-battery-1:before {
+  content: "\f243"; }
+
+.fa.fa-battery-0:before {
+  content: "\f244"; }
+
+.fa.fa-object-group {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-object-ungroup {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-sticky-note-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-sticky-note-o:before {
+  content: "\f249"; }
+
+.fa.fa-cc-jcb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-cc-diners-club {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-clone {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hourglass-o:before {
+  content: "\f254"; }
+
+.fa.fa-hourglass-1:before {
+  content: "\f251"; }
+
+.fa.fa-hourglass-2:before {
+  content: "\f252"; }
+
+.fa.fa-hourglass-3:before {
+  content: "\f253"; }
+
+.fa.fa-hand-rock-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-rock-o:before {
+  content: "\f255"; }
+
+.fa.fa-hand-grab-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-grab-o:before {
+  content: "\f255"; }
+
+.fa.fa-hand-paper-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-paper-o:before {
+  content: "\f256"; }
+
+.fa.fa-hand-stop-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-stop-o:before {
+  content: "\f256"; }
+
+.fa.fa-hand-scissors-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-scissors-o:before {
+  content: "\f257"; }
+
+.fa.fa-hand-lizard-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-lizard-o:before {
+  content: "\f258"; }
+
+.fa.fa-hand-spock-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-spock-o:before {
+  content: "\f259"; }
+
+.fa.fa-hand-pointer-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-pointer-o:before {
+  content: "\f25a"; }
+
+.fa.fa-hand-peace-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-hand-peace-o:before {
+  content: "\f25b"; }
+
+.fa.fa-registered {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-creative-commons {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-gg {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-gg-circle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-odnoklassniki {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-odnoklassniki-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-odnoklassniki-square:before {
+  content: "\f264"; }
+
+.fa.fa-get-pocket {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wikipedia-w {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-safari {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-chrome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-firefox {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-opera {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-internet-explorer {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-television:before {
+  content: "\f26c"; }
+
+.fa.fa-contao {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-500px {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-amazon {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-calendar-plus-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-calendar-plus-o:before {
+  content: "\f271"; }
+
+.fa.fa-calendar-minus-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-calendar-minus-o:before {
+  content: "\f272"; }
+
+.fa.fa-calendar-times-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-calendar-times-o:before {
+  content: "\f273"; }
+
+.fa.fa-calendar-check-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-calendar-check-o:before {
+  content: "\f274"; }
+
+.fa.fa-map-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-map-o:before {
+  content: "\f279"; }
+
+.fa.fa-commenting:before {
+  content: "\f4ad"; }
+
+.fa.fa-commenting-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-commenting-o:before {
+  content: "\f4ad"; }
+
+.fa.fa-houzz {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-vimeo {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-vimeo:before {
+  content: "\f27d"; }
+
+.fa.fa-black-tie {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fonticons {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-reddit-alien {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-edge {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-credit-card-alt:before {
+  content: "\f09d"; }
+
+.fa.fa-codiepie {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-modx {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fort-awesome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-usb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-product-hunt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-mixcloud {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-scribd {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-pause-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-pause-circle-o:before {
+  content: "\f28b"; }
+
+.fa.fa-stop-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-stop-circle-o:before {
+  content: "\f28d"; }
+
+.fa.fa-bluetooth {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-bluetooth-b {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-gitlab {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpbeginner {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpforms {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-envira {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wheelchair-alt:before {
+  content: "\f368"; }
+
+.fa.fa-question-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-question-circle-o:before {
+  content: "\f059"; }
+
+.fa.fa-volume-control-phone:before {
+  content: "\f2a0"; }
+
+.fa.fa-asl-interpreting:before {
+  content: "\f2a3"; }
+
+.fa.fa-deafness:before {
+  content: "\f2a4"; }
+
+.fa.fa-hard-of-hearing:before {
+  content: "\f2a4"; }
+
+.fa.fa-glide {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-glide-g {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-signing:before {
+  content: "\f2a7"; }
+
+.fa.fa-viadeo {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-viadeo-square:before {
+  content: "\f2aa"; }
+
+.fa.fa-snapchat {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-ghost:before {
+  content: "\f2ab"; }
+
+.fa.fa-snapchat-square {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-snapchat-square:before {
+  content: "\f2ad"; }
+
+.fa.fa-pied-piper {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-first-order {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-yoast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-themeisle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-official:before {
+  content: "\f2b3"; }
+
+.fa.fa-google-plus-circle {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-google-plus-circle:before {
+  content: "\f2b3"; }
+
+.fa.fa-font-awesome {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-fa:before {
+  content: "\f2b4"; }
+
+.fa.fa-handshake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-handshake-o:before {
+  content: "\f2b5"; }
+
+.fa.fa-envelope-open-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-envelope-open-o:before {
+  content: "\f2b6"; }
+
+.fa.fa-linode {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-address-book-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-book-o:before {
+  content: "\f2b9"; }
+
+.fa.fa-vcard:before {
+  content: "\f2bb"; }
+
+.fa.fa-address-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-address-card-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-vcard-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-vcard-o:before {
+  content: "\f2bb"; }
+
+.fa.fa-user-circle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-circle-o:before {
+  content: "\f2bd"; }
+
+.fa.fa-user-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-user-o:before {
+  content: "\f007"; }
+
+.fa.fa-id-badge {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license:before {
+  content: "\f2c2"; }
+
+.fa.fa-id-card-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-id-card-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-drivers-license-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-drivers-license-o:before {
+  content: "\f2c2"; }
+
+.fa.fa-quora {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-free-code-camp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-telegram {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-thermometer-4:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer:before {
+  content: "\f2c7"; }
+
+.fa.fa-thermometer-3:before {
+  content: "\f2c8"; }
+
+.fa.fa-thermometer-2:before {
+  content: "\f2c9"; }
+
+.fa.fa-thermometer-1:before {
+  content: "\f2ca"; }
+
+.fa.fa-thermometer-0:before {
+  content: "\f2cb"; }
+
+.fa.fa-bathtub:before {
+  content: "\f2cd"; }
+
+.fa.fa-s15:before {
+  content: "\f2cd"; }
+
+.fa.fa-window-maximize {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-restore {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle:before {
+  content: "\f410"; }
+
+.fa.fa-window-close-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-window-close-o:before {
+  content: "\f410"; }
+
+.fa.fa-times-rectangle-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-times-rectangle-o:before {
+  content: "\f410"; }
+
+.fa.fa-bandcamp {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-grav {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-etsy {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-imdb {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-ravelry {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-eercast:before {
+  content: "\f2da"; }
+
+.fa.fa-snowflake-o {
+  font-family: 'Font Awesome 6 Free';
+  font-weight: 400; }
+
+.fa.fa-snowflake-o:before {
+  content: "\f2dc"; }
+
+.fa.fa-superpowers {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-wpexplorer {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
+
+.fa.fa-meetup {
+  font-family: 'Font Awesome 6 Brands';
+  font-weight: 400; }
diff --git a/deps/font-awesome-6.4.2/css/v4-shims.min.css b/deps/font-awesome-6.4.2/css/v4-shims.min.css
new file mode 100644
index 0000000..64e4e8d
--- /dev/null
+++ b/deps/font-awesome-6.4.2/css/v4-shims.min.css
@@ -0,0 +1,6 @@
+/*!
+ * Font Awesome Free 6.4.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2023 Fonticons, Inc.
+ */
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diff --git a/deps/headroom-0.11.0/headroom.min.js b/deps/headroom-0.11.0/headroom.min.js
new file mode 100644
index 0000000..433069f
--- /dev/null
+++ b/deps/headroom-0.11.0/headroom.min.js
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+/*!
+ * headroom.js v0.11.0 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(n):(t=t||self).Headroom=n()}(this,function(){"use strict";function t(){return"undefined"!=typeof window}function d(t){return function(t){return t&&t.document&&function(t){return 9===t.nodeType}(t.document)}(t)?function(t){var n=t.document,o=n.body,s=n.documentElement;return{scrollHeight:function(){return Math.max(o.scrollHeight,s.scrollHeight,o.offsetHeight,s.offsetHeight,o.clientHeight,s.clientHeight)},height:function(){return t.innerHeight||s.clientHeight||o.clientHeight},scrollY:function(){return void 0!==t.pageYOffset?t.pageYOffset:(s||o.parentNode||o).scrollTop}}}(t):function(t){return{scrollHeight:function(){return Math.max(t.scrollHeight,t.offsetHeight,t.clientHeight)},height:function(){return Math.max(t.offsetHeight,t.clientHeight)},scrollY:function(){return t.scrollTop}}}(t)}function n(t,s,e){var n,o=function(){var n=!1;try{var t={get passive(){n=!0}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){n=!1}return n}(),i=!1,r=d(t),l=r.scrollY(),a={};function c(){var t=Math.round(r.scrollY()),n=r.height(),o=r.scrollHeight();a.scrollY=t,a.lastScrollY=l,a.direction=l<t?"down":"up",a.distance=Math.abs(t-l),a.isOutOfBounds=t<0||o<t+n,a.top=t<=s.offset,a.bottom=o<=t+n,a.toleranceExceeded=a.distance>s.tolerance[a.direction],e(a),l=t,i=!1}function h(){i||(i=!0,n=requestAnimationFrame(c))}var u=!!o&&{passive:!0,capture:!1};return t.addEventListener("scroll",h,u),c(),{destroy:function(){cancelAnimationFrame(n),t.removeEventListener("scroll",h,u)}}}function o(t,n){n=n||{},Object.assign(this,o.options,n),this.classes=Object.assign({},o.options.classes,n.classes),this.elem=t,this.tolerance=function(t){return t===Object(t)?t:{down:t,up:t}}(this.tolerance),this.initialised=!1,this.frozen=!1}return o.prototype={constructor:o,init:function(){return o.cutsTheMustard&&!this.initialised&&(this.addClass("initial"),this.initialised=!0,setTimeout(function(t){t.scrollTracker=n(t.scroller,{offset:t.offset,tolerance:t.tolerance},t.update.bind(t))},100,this)),this},destroy:function(){this.initialised=!1,Object.keys(this.classes).forEach(this.removeClass,this),this.scrollTracker.destroy()},unpin:function(){!this.hasClass("pinned")&&this.hasClass("unpinned")||(this.addClass("unpinned"),this.removeClass("pinned"),this.onUnpin&&this.onUnpin.call(this))},pin:function(){this.hasClass("unpinned")&&(this.addClass("pinned"),this.removeClass("unpinned"),this.onPin&&this.onPin.call(this))},freeze:function(){this.frozen=!0,this.addClass("frozen")},unfreeze:function(){this.frozen=!1,this.removeClass("frozen")},top:function(){this.hasClass("top")||(this.addClass("top"),this.removeClass("notTop"),this.onTop&&this.onTop.call(this))},notTop:function(){this.hasClass("notTop")||(this.addClass("notTop"),this.removeClass("top"),this.onNotTop&&this.onNotTop.call(this))},bottom:function(){this.hasClass("bottom")||(this.addClass("bottom"),this.removeClass("notBottom"),this.onBottom&&this.onBottom.call(this))},notBottom:function(){this.hasClass("notBottom")||(this.addClass("notBottom"),this.removeClass("bottom"),this.onNotBottom&&this.onNotBottom.call(this))},shouldUnpin:function(t){return"down"===t.direction&&!t.top&&t.toleranceExceeded},shouldPin:function(t){return"up"===t.direction&&t.toleranceExceeded||t.top},addClass:function(t){this.elem.classList.add.apply(this.elem.classList,this.classes[t].split(" "))},removeClass:function(t){this.elem.classList.remove.apply(this.elem.classList,this.classes[t].split(" "))},hasClass:function(t){return this.classes[t].split(" ").every(function(t){return this.classList.contains(t)},this.elem)},update:function(t){t.isOutOfBounds||!0!==this.frozen&&(t.top?this.top():this.notTop(),t.bottom?this.bottom():this.notBottom(),this.shouldUnpin(t)?this.unpin():this.shouldPin(t)&&this.pin())}},o.options={tolerance:{up:0,down:0},offset:0,scroller:t()?window:null,classes:{frozen:"headroom--frozen",pinned:"headroom--pinned",unpinned:"headroom--unpinned",top:"headroom--top",notTop:"headroom--not-top",bottom:"headroom--bottom",notBottom:"headroom--not-bottom",initial:"headroom"}},o.cutsTheMustard=!!(t()&&function(){}.bind&&"classList"in document.documentElement&&Object.assign&&Object.keys&&requestAnimationFrame),o});
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new file mode 100644
index 0000000..17f70c9
--- /dev/null
+++ b/deps/headroom-0.11.0/jQuery.headroom.min.js
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+/*!
+ * headroom.js v0.9.4 - Give your page some headroom. Hide your header until you need it
+ * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js
+ * License: MIT
+ */
+
+!function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery);
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new file mode 100644
index 0000000..fb63a6a
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+++ b/deps/search-1.0.0/autocomplete.jquery.min.js
@@ -0,0 +1,7 @@
+/*!
+ * autocomplete.js 0.38.0
+ * https://github.com/algolia/autocomplete.js
+ * Copyright 2020 Algolia, Inc. and other contributors; Licensed MIT
+ */
+!function(a){function b(d){if(c[d])return c[d].exports;var e=c[d]={exports:{},id:d,loaded:!1};return a[d].call(e.exports,e,e.exports,b),e.loaded=!0,e.exports}var c={};b.m=a,b.c=c,b.p="",b(0)}([function(a,b,c){"use strict";a.exports=c(1)},function(a,b,c){"use strict";var d=c(2),e=c(3);d.element=e;var f=c(4);f.isArray=e.isArray,f.isFunction=e.isFunction,f.isObject=e.isPlainObject,f.bind=e.proxy,f.each=function(a,b){function c(a,c){return b(c,a)}e.each(a,c)},f.map=e.map,f.mixin=e.extend,f.Event=e.Event;var g,h,i,j=c(5),k=c(6);g=e.fn.autocomplete,h="aaAutocomplete",i={initialize:function(a,b){function c(){var c,d=e(this),f=new k({el:d});c=new j({input:d,eventBus:f,dropdownMenuContainer:a.dropdownMenuContainer,hint:void 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f=document.createElement("div");f.appendChild(document.createTextNode(c));var g=document.createElement("div");return g.appendChild(document.createTextNode(a)),g.innerHTML.replace(RegExp(d(e.innerHTML),"g"),b).replace(RegExp(d(f.innerHTML),"g"),c)}}},function(a,b,c){"use strict";function d(a){var b,c;if(a=a||{},a.input||i.error("missing input"),this.isActivated=!1,this.debug=!!a.debug,this.autoselect=!!a.autoselect,this.autoselectOnBlur=!!a.autoselectOnBlur,this.openOnFocus=!!a.openOnFocus,this.minLength=i.isNumber(a.minLength)?a.minLength:1,this.autoWidth=void 0===a.autoWidth||!!a.autoWidth,this.clearOnSelected=!!a.clearOnSelected,this.tabAutocomplete=void 0===a.tabAutocomplete||!!a.tabAutocomplete,a.hint=!!a.hint,a.hint&&a.appendTo)throw new Error("[autocomplete.js] hint and appendTo options can't be used at the same time");this.css=a.css=i.mixin({},o,a.appendTo?o.appendTo:{}),this.cssClasses=a.cssClasses=i.mixin({},o.defaultClasses,a.cssClasses||{}),this.cssClasses.prefix=a.cssClasses.formattedPrefix=i.formatPrefix(this.cssClasses.prefix,this.cssClasses.noPrefix),this.listboxId=a.listboxId=[this.cssClasses.root,"listbox",i.getUniqueId()].join("-");var f=e(a);this.$node=f.wrapper;var g=this.$input=f.input;b=f.menu,c=f.hint,a.dropdownMenuContainer&&j.element(a.dropdownMenuContainer).css("position","relative").append(b.css("top","0")),g.on("blur.aa",function(a){var c=document.activeElement;i.isMsie()&&(b[0]===c||b[0].contains(c))&&(a.preventDefault(),a.stopImmediatePropagation(),i.defer(function(){g.focus()}))}),b.on("mousedown.aa",function(a){a.preventDefault()}),this.eventBus=a.eventBus||new k({el:g}),this.dropdown=new d.Dropdown({appendTo:a.appendTo,wrapper:this.$node,menu:b,datasets:a.datasets,templates:a.templates,cssClasses:a.cssClasses,minLength:this.minLength}).onSync("suggestionClicked",this._onSuggestionClicked,this).onSync("cursorMoved",this._onCursorMoved,this).onSync("cursorRemoved",this._onCursorRemoved,this).onSync("opened",this._onOpened,this).onSync("closed",this._onClosed,this).onSync("shown",this._onShown,this).onSync("empty",this._onEmpty,this).onSync("redrawn",this._onRedrawn,this).onAsync("datasetRendered",this._onDatasetRendered,this),this.input=new 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g=n.dropdown.replace("%PREFIX%",a.cssClasses.prefix).replace("%DROPDOWN_MENU%",a.cssClasses.dropdownMenu);d=j.element(g).css(a.css.dropdown).attr({role:"listbox",id:a.listboxId}),a.templates&&a.templates.dropdownMenu&&d.html(i.templatify(a.templates.dropdownMenu)()),e=b.clone().css(a.css.hint).css(f(b)),e.val("").addClass(i.className(a.cssClasses.prefix,a.cssClasses.hint,!0)).removeAttr("id name placeholder required").prop("readonly",!0).attr({"aria-hidden":"true",autocomplete:"off",spellcheck:"false",tabindex:-1}),e.removeData&&e.removeData(),b.data(h,{"aria-autocomplete":b.attr("aria-autocomplete"),"aria-expanded":b.attr("aria-expanded"),"aria-owns":b.attr("aria-owns"),autocomplete:b.attr("autocomplete"),dir:b.attr("dir"),role:b.attr("role"),spellcheck:b.attr("spellcheck"),style:b.attr("style"),type:b.attr("type")}),b.addClass(i.className(a.cssClasses.prefix,a.cssClasses.input,!0)).attr({autocomplete:"off",spellcheck:!1,role:"combobox","aria-autocomplete":a.datasets&&a.datasets[0]&&a.datasets[0].displayKey?"both":"list","aria-expanded":"false","aria-label":a.ariaLabel,"aria-owns":a.listboxId}).css(a.hint?a.css.input:a.css.inputWithNoHint);try{b.attr("dir")||b.attr("dir","auto")}catch(a){}return c=a.appendTo?c.appendTo(j.element(a.appendTo).eq(0)).eq(0):b.wrap(c).parent(),c.prepend(a.hint?e:null).append(d),{wrapper:c,input:b,hint:e,menu:d}}function f(a){return{backgroundAttachment:a.css("background-attachment"),backgroundClip:a.css("background-clip"),backgroundColor:a.css("background-color"),backgroundImage:a.css("background-image"),backgroundOrigin:a.css("background-origin"),backgroundPosition:a.css("background-position"),backgroundRepeat:a.css("background-repeat"),backgroundSize:a.css("background-size")}}function g(a,b){var c=a.find(i.className(b.prefix,b.input));i.each(c.data(h),function(a,b){void 0===a?c.removeAttr(b):c.attr(b,a)}),c.detach().removeClass(i.className(b.prefix,b.input,!0)).insertAfter(a),c.removeData&&c.removeData(h),a.remove()}var h="aaAttrs",i=c(4),j=c(2),k=c(6),l=c(7),m=c(16),n=c(18),o=c(19);i.mixin(d.prototype,{_bindKeyboardShortcuts:function(a){if(a.keyboardShortcuts){var b=this.$input,c=[];i.each(a.keyboardShortcuts,function(a){"string"==typeof a&&(a=a.toUpperCase().charCodeAt(0)),c.push(a)}),j.element(document).keydown(function(a){var d=a.target||a.srcElement,e=d.tagName;if(!d.isContentEditable&&"INPUT"!==e&&"SELECT"!==e&&"TEXTAREA"!==e){var f=a.which||a.keyCode;c.indexOf(f)!==-1&&(b.focus(),a.stopPropagation(),a.preventDefault())}})}},_onSuggestionClicked:function(a,b){var c,d={selectionMethod:"click"};(c=this.dropdown.getDatumForSuggestion(b))&&this._select(c,d)},_onCursorMoved:function(a,b){var c=this.dropdown.getDatumForCursor(),d=this.dropdown.getCurrentCursor().attr("id");this.input.setActiveDescendant(d),c&&(b&&this.input.setInputValue(c.value,!0),this.eventBus.trigger("cursorchanged",c.raw,c.datasetName))},_onCursorRemoved:function(){this.input.resetInputValue(),this._updateHint(),this.eventBus.trigger("cursorremoved")},_onDatasetRendered:function(){this._updateHint(),this.eventBus.trigger("updated")},_onOpened:function(){this._updateHint(),this.input.expand(),this.eventBus.trigger("opened")},_onEmpty:function(){this.eventBus.trigger("empty")},_onRedrawn:function(){this.$node.css("top","0px"),this.$node.css("left","0px");var a=this.$input[0].getBoundingClientRect();this.autoWidth&&this.$node.css("width",a.width+"px");var b=this.$node[0].getBoundingClientRect(),c=a.bottom-b.top;this.$node.css("top",c+"px");var d=a.left-b.left;this.$node.css("left",d+"px"),this.eventBus.trigger("redrawn")},_onShown:function(){this.eventBus.trigger("shown"),this.autoselect&&this.dropdown.cursorTopSuggestion()},_onClosed:function(){this.input.clearHint(),this.input.removeActiveDescendant(),this.input.collapse(),this.eventBus.trigger("closed")},_onFocused:function(){if(this.isActivated=!0,this.openOnFocus){var a=this.input.getQuery();a.length>=this.minLength?this.dropdown.update(a):this.dropdown.empty(),this.dropdown.open()}},_onBlurred:function(){var a,b;a=this.dropdown.getDatumForCursor(),b=this.dropdown.getDatumForTopSuggestion();var c={selectionMethod:"blur"};this.debug||(this.autoselectOnBlur&&a?this._select(a,c):this.autoselectOnBlur&&b?this._select(b,c):(this.isActivated=!1,this.dropdown.empty(),this.dropdown.close()))},_onEnterKeyed:function(a,b){var c,d;c=this.dropdown.getDatumForCursor(),d=this.dropdown.getDatumForTopSuggestion();var e={selectionMethod:"enterKey"};c?(this._select(c,e),b.preventDefault()):this.autoselect&&d&&(this._select(d,e),b.preventDefault())},_onTabKeyed:function(a,b){if(!this.tabAutocomplete)return void this.dropdown.close();var c,d={selectionMethod:"tabKey"};(c=this.dropdown.getDatumForCursor())?(this._select(c,d),b.preventDefault()):this._autocomplete(!0)},_onEscKeyed:function(){this.dropdown.close(),this.input.resetInputValue()},_onUpKeyed:function(){var a=this.input.getQuery();this.dropdown.isEmpty&&a.length>=this.minLength?this.dropdown.update(a):this.dropdown.moveCursorUp(),this.dropdown.open()},_onDownKeyed:function(){var a=this.input.getQuery();this.dropdown.isEmpty&&a.length>=this.minLength?this.dropdown.update(a):this.dropdown.moveCursorDown(),this.dropdown.open()},_onLeftKeyed:function(){"rtl"===this.dir&&this._autocomplete()},_onRightKeyed:function(){"ltr"===this.dir&&this._autocomplete()},_onQueryChanged:function(a,b){this.input.clearHintIfInvalid(),b.length>=this.minLength?this.dropdown.update(b):this.dropdown.empty(),this.dropdown.open(),this._setLanguageDirection()},_onWhitespaceChanged:function(){this._updateHint(),this.dropdown.open()},_setLanguageDirection:function(){var a=this.input.getLanguageDirection();this.dir!==a&&(this.dir=a,this.$node.css("direction",a),this.dropdown.setLanguageDirection(a))},_updateHint:function(){var a,b,c,d,e,f;a=this.dropdown.getDatumForTopSuggestion(),a&&this.dropdown.isVisible()&&!this.input.hasOverflow()?(b=this.input.getInputValue(),c=l.normalizeQuery(b),d=i.escapeRegExChars(c),e=new 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a=this.input.getInputValue();a.length>=this.minLength?this.dropdown.update(a):this.dropdown.empty()}this.dropdown.open()},close:function(){this.dropdown.close()},setVal:function(a){a=i.toStr(a),this.isActivated?this.input.setInputValue(a):(this.input.setQuery(a),this.input.setInputValue(a,!0)),this._setLanguageDirection()},getVal:function(){return this.input.getQuery()},destroy:function(){this.input.destroy(),this.dropdown.destroy(),g(this.$node,this.cssClasses),this.$node=null},getWrapper:function(){return this.dropdown.$container[0]}}),d.Dropdown=m,d.Input=l,d.sources=c(20),a.exports=d},function(a,b,c){"use strict";function d(a){a&&a.el||e.error("EventBus initialized without el"),this.$el=f.element(a.el)}var e=c(4),f=c(2);e.mixin(d.prototype,{trigger:function(a,b,c,d){var f=e.Event("autocomplete:"+a);return this.$el.trigger(f,[b,c,d]),f}}),a.exports=d},function(a,b,c){"use strict";function d(a){var b,c,d,f,g=this;a=a||{},a.input||i.error("input is 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b=h[a.which||a.keyCode];this._managePreventDefault(b,a),b&&this._shouldTrigger(b,a)&&this.trigger(b+"Keyed",a)},_onInput:function(){this._checkInputValue()},_managePreventDefault:function(a,b){var c,d,e;switch(a){case"tab":d=this.getHint(),e=this.getInputValue(),c=d&&d!==e&&!g(b);break;case"up":case"down":c=!g(b);break;default:c=!1}c&&b.preventDefault()},_shouldTrigger:function(a,b){var c;switch(a){case"tab":c=!g(b);break;default:c=!0}return c},_checkInputValue:function(){var a,b,c;a=this.getInputValue(),b=f(a,this.query),c=!(!b||!this.query)&&this.query.length!==a.length,this.query=a,b?c&&this.trigger("whitespaceChanged",this.query):this.trigger("queryChanged",this.query)},focus:function(){this.$input.focus()},blur:function(){this.$input.blur()},getQuery:function(){return this.query},setQuery:function(a){this.query=a},getInputValue:function(){return this.$input.val()},setInputValue:function(a,b){void 0===a&&(a=this.query),this.$input.val(a),b?this.clearHint():this._checkInputValue()},expand:function(){this.$input.attr("aria-expanded","true")},collapse:function(){this.$input.attr("aria-expanded","false")},setActiveDescendant:function(a){this.$input.attr("aria-activedescendant",a)},removeActiveDescendant:function(){this.$input.removeAttr("aria-activedescendant")},resetInputValue:function(){this.setInputValue(this.query,!0)},getHint:function(){return this.$hint.val()},setHint:function(a){this.$hint.val(a)},clearHint:function(){this.setHint("")},clearHintIfInvalid:function(){var a,b,c,d;a=this.getInputValue(),b=this.getHint(),c=a!==b&&0===b.indexOf(a),(d=""!==a&&c&&!this.hasOverflow())||this.clearHint()},getLanguageDirection:function(){return(this.$input.css("direction")||"ltr").toLowerCase()},hasOverflow:function(){var a=this.$input.width()-2;return this.$overflowHelper.text(this.getInputValue()),this.$overflowHelper.width()>=a},isCursorAtEnd:function(){var a,b,c;return 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+var c=[].slice.call(arguments,1);this.cacheSuggestions(a,b,c),this._render.apply(this,[a,b].concat(c))}}if(this.query=a,this.canceled=!1,this.shouldFetchFromCache(a))b.apply(this,[this.cachedSuggestions].concat(this.cachedRenderExtraArgs));else{var c=this,d=function(){c.canceled||c.source(a,b.bind(c))};if(this.debounce){var e=function(){c.debounceTimeout=null,d()};clearTimeout(this.debounceTimeout),this.debounceTimeout=setTimeout(e,this.debounce)}else d()}},cacheSuggestions:function(a,b,c){this.cachedQuery=a,this.cachedSuggestions=b,this.cachedRenderExtraArgs=c},shouldFetchFromCache:function(a){return this.cache&&this.cachedQuery===a&&this.cachedSuggestions&&this.cachedSuggestions.length},clearCachedSuggestions:function(){delete this.cachedQuery,delete this.cachedSuggestions,delete this.cachedRenderExtraArgs},cancel:function(){this.canceled=!0},clear:function(){this.$el&&(this.cancel(),this.$el.empty(),this.trigger("rendered",""))},isEmpty:function(){return this._isEmpty},destroy:function(){this.clearCachedSuggestions(),this.$el=null}}),a.exports=d},function(a,b){"use strict";a.exports={wrapper:'<span class="%ROOT%"></span>',dropdown:'<span class="%PREFIX%%DROPDOWN_MENU%"></span>',dataset:'<div class="%PREFIX%%DATASET%-%CLASS%"></div>',suggestions:'<span class="%PREFIX%%SUGGESTIONS%"></span>',suggestion:'<div class="%PREFIX%%SUGGESTION%"></div>'}},function(a,b,c){"use strict";var d=c(4),e={wrapper:{position:"relative",display:"inline-block"},hint:{position:"absolute",top:"0",left:"0",borderColor:"transparent",boxShadow:"none",opacity:"1"},input:{position:"relative",verticalAlign:"top",backgroundColor:"transparent"},inputWithNoHint:{position:"relative",verticalAlign:"top"},dropdown:{position:"absolute",top:"100%",left:"0",zIndex:"100",display:"none"},suggestions:{display:"block"},suggestion:{whiteSpace:"nowrap",cursor:"pointer"},suggestionChild:{whiteSpace:"normal"},ltr:{left:"0",right:"auto"},rtl:{left:"auto",right:"0"},defaultClasses:{root:"algolia-autocomplete",prefix:"aa",noPrefix:!1,dropdownMenu:"dropdown-menu",input:"input",hint:"hint",suggestions:"suggestions",suggestion:"suggestion",cursor:"cursor",dataset:"dataset",empty:"empty"},appendTo:{wrapper:{position:"absolute",zIndex:"100",display:"none"},input:{},inputWithNoHint:{},dropdown:{display:"block"}}};d.isMsie()&&d.mixin(e.input,{backgroundImage:"url(data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)"}),d.isMsie()&&d.isMsie()<=7&&d.mixin(e.input,{marginTop:"-1px"}),a.exports=e},function(a,b,c){"use strict";a.exports={hits:c(21),popularIn:c(24)}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23),g=function(){function a(a,d){return window.Promise.resolve().then(function(){return b.length&&(e=a.search(b),b=[]),e}).then(function(a){if(a)return c=a.results,c[d]})}var b=[],c=[],e=window.Promise.resolve();return function(c,e){return function(f,g){a(c.as,b.push({indexName:c.indexName,query:f,params:e})-1).then(function(a){a&&g(a.hits,a)}).catch(function(a){d.error(a.message)})}}}();a.exports=function(a,b){var c=f(a.as._ua);if(c&&c[0]>=3&&c[1]>20){var d="autocomplete.js "+e;a.as._ua.indexOf(d)===-1&&(a.as._ua+="; "+d)}return g(a,b)}},function(a,b){a.exports="0.38.0"},function(a,b){"use strict";a.exports=function(a){var b=a.match(/Algolia for JavaScript \((\d+\.)(\d+\.)(\d+)\)/)||a.match(/Algolia for vanilla JavaScript (\d+\.)(\d+\.)(\d+)/);if(b)return[b[1],b[2],b[3]]}},function(a,b,c){"use strict";var d=c(4),e=c(22),f=c(23);a.exports=function(a,b,c,g){function h(h,i){a.search(h,b,function(a,h){if(a)return void d.error(a.message);if(h.hits.length>0){var l=h.hits[0],m=d.mixin({hitsPerPage:0},c);delete m.source,delete m.index;var n=f(k.as._ua);return n&&n[0]>=3&&n[1]>20&&(b.additionalUA="autocomplete.js "+e),void k.search(j(l),m,function(a,b){if(a)return void d.error(a.message);var c=[];if(g.includeAll){var e=g.allTitle||"All departments";c.push(d.mixin({facet:{value:e,count:b.nbHits}},d.cloneDeep(l)))}d.each(b.facets,function(a,b){d.each(a,function(a,e){c.push(d.mixin({facet:{facet:b,value:e,count:a}},d.cloneDeep(l)))})});for(var f=1;f<h.hits.length;++f)c.push(h.hits[f]);i(c,h)})}i([])})}var i=f(a.as._ua);if(i&&i[0]>=3&&i[1]>20&&(b=b||{},b.additionalUA="autocomplete.js "+e),!c.source)return d.error("Missing 'source' key");var j=d.isFunction(c.source)?c.source:function(a){return a[c.source]};if(!c.index)return d.error("Missing 'index' key");var k=c.index;return g=g||{},h}}]);
\ No newline at end of file
diff --git a/deps/search-1.0.0/fuse.min.js b/deps/search-1.0.0/fuse.min.js
new file mode 100644
index 0000000..7def598
--- /dev/null
+++ b/deps/search-1.0.0/fuse.min.js
@@ -0,0 +1,9 @@
+/**
+ * Fuse.js v6.4.6 - Lightweight fuzzy-search (http://fusejs.io)
+ *
+ * Copyright (c) 2021 Kiro Risk (http://kiro.me)
+ * All Rights Reserved. Apache Software License 2.0
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ */
+var e,t;e=this,t=function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(t)}function t(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function n(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}function r(e,t,r){return t&&n(e.prototype,t),r&&n(e,r),e}function i(e,t,n){return t in e?Object.defineProperty(e,t,{value:n,enumerable:!0,configurable:!0,writable:!0}):e[t]=n,e}function o(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),n.push.apply(n,r)}return n}function c(e){for(var t=1;t<arguments.length;t++){var 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c=t.searchIn(n),a=c.isMatch,s=c.score,u=c.indices;a&&r.push({item:n,idx:i,matches:[{score:s,value:n,norm:o,indices:u}]})}})),r}},{key:"_searchLogical",value:function(e){var t=this,n=function(e,t){var n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:{},r=n.auto,i=void 0===r||r,o=function e(n){var r=Object.keys(n),o=ae(n);if(!o&&r.length>1&&!ce(n))return e(ue(n));if(se(n)){var c=o?n[ie]:r[0],a=o?n[oe]:n[c];if(!g(a))throw new Error(x(c));var s={keyId:j(c),pattern:a};return i&&(s.searcher=te(a,t)),s}var u={children:[],operator:r[0]};return r.forEach((function(t){var r=n[t];v(r)&&r.forEach((function(t){u.children.push(e(t))}))})),u};return ce(e)||(e=ue(e)),o(e)}(e,this.options),r=this._myIndex.records,i={},o=[];return r.forEach((function(e){var r=e.$,c=e.i;if(k(r)){var a=function e(n,r,i){if(!n.children){var o=n.keyId,c=n.searcher,a=t._findMatches({key:t._keyStore.get(o),value:t._myIndex.getValueForItemAtKeyId(r,o),searcher:c});return a&&a.length?[{idx:i,item:r,matches:a}]:[]}switch(n.operator){case ne:for(var s=[],u=0,h=n.children.length;u<h;u+=1){var f=e(n.children[u],r,i);if(!f.length)return[];s.push.apply(s,l(f))}return s;case re:for(var d=[],v=0,g=n.children.length;v<g;v+=1){var y=e(n.children[v],r,i);if(y.length){d.push.apply(d,l(y));break}}return d}}(n,r,c);a.length&&(i[c]||(i[c]={idx:c,item:r,matches:[]},o.push(i[c])),a.forEach((function(e){var t,n=e.matches;(t=i[c].matches).push.apply(t,l(n))})))}})),o}},{key:"_searchObjectList",value:function(e){var t=this,n=te(e,this.options),r=this._myIndex,i=r.keys,o=r.records,c=[];return o.forEach((function(e){var r=e.$,o=e.i;if(k(r)){var a=[];i.forEach((function(e,i){a.push.apply(a,l(t._findMatches({key:e,value:r[i],searcher:n})))})),a.length&&c.push({idx:o,item:r,matches:a})}})),c}},{key:"_findMatches",value:function(e){var t=e.key,n=e.value,r=e.searcher;if(!k(n))return[];var i=[];if(v(n))n.forEach((function(e){var n=e.v,o=e.i,c=e.n;if(k(n)){var a=r.searchIn(n),s=a.isMatch,u=a.score,h=a.indices;s&&i.push({score:u,key:t,value:n,idx:o,norm:c,indices:h})}}));else{var o=n.v,c=n.n,a=r.searchIn(o),s=a.isMatch,u=a.score,h=a.indices;s&&i.push({score:u,key:t,value:o,norm:c,indices:h})}return i}}]),e}();return ve.version="6.4.6",ve.createIndex=$,ve.parseIndex=function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=t.getFn,r=void 0===n?A.getFn:n,i=e.keys,o=e.records,c=new E({getFn:r});return c.setKeys(i),c.setIndexRecords(o),c},ve.config=A,function(){ee.push.apply(ee,arguments)}(Z),ve},"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e=e||self).Fuse=t();
\ No newline at end of file
diff --git a/deps/search-1.0.0/mark.min.js b/deps/search-1.0.0/mark.min.js
new file mode 100644
index 0000000..1eea053
--- /dev/null
+++ b/deps/search-1.0.0/mark.min.js
@@ -0,0 +1,7 @@
+/*!***************************************************
+* mark.js v8.11.1
+* https://markjs.io/
+* Copyright (c) 2014–2018, Julian Kühnel
+* Released under the MIT license https://git.io/vwTVl
+*****************************************************/
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):e.Mark=t()}(this,function(){"use strict";var e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e},t=function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")},n=function(){function e(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(t,n,r){return n&&e(t.prototype,n),r&&e(t,r),t}}(),r=Object.assign||function(e){for(var t=1;t<arguments.length;t++){var n=arguments[t];for(var r in n)Object.prototype.hasOwnProperty.call(n,r)&&(e[r]=n[r])}return e},i=function(){function e(n){var r=!(arguments.length>1&&void 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t=e.getAttribute("src").trim();return"about:blank"===e.contentWindow.location.href&&"about:blank"!==t&&t}},{key:"observeIframeLoad",value:function(e,t,n){var r=this,i=!1,o=null,a=function a(){if(!i){i=!0,clearTimeout(o);try{r.isIframeBlank(e)||(e.removeEventListener("load",a),r.getIframeContents(e,t,n))}catch(e){n()}}};e.addEventListener("load",a),o=setTimeout(a,this.iframesTimeout)}},{key:"onIframeReady",value:function(e,t,n){try{"complete"===e.contentWindow.document.readyState?this.isIframeBlank(e)?this.observeIframeLoad(e,t,n):this.getIframeContents(e,t,n):this.observeIframeLoad(e,t,n)}catch(e){n()}}},{key:"waitForIframes",value:function(e,t){var n=this,r=0;this.forEachIframe(e,function(){return!0},function(e){r++,n.waitForIframes(e.querySelector("html"),function(){--r||t()})},function(e){e||t()})}},{key:"forEachIframe",value:function(t,n,r){var i=this,o=arguments.length>3&&void 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0!==arguments[3]?arguments[3]:function(){},o=this.getContexts(),a=o.length;a||i(),o.forEach(function(o){var s=function(){r.iterateThroughNodes(e,o,t,n,function(){--a<=0&&i()})};r.iframes?r.waitForIframes(o,s):s()})}}],[{key:"matches",value:function(e,t){var n="string"==typeof t?[t]:t,r=e.matches||e.matchesSelector||e.msMatchesSelector||e.mozMatchesSelector||e.oMatchesSelector||e.webkitMatchesSelector;if(r){var i=!1;return n.every(function(t){return!r.call(e,t)||(i=!0,!1)}),i}return!1}}]),e}(),o=function(){function o(e){t(this,o),this.ctx=e,this.ie=!1;var n=window.navigator.userAgent;(n.indexOf("MSIE")>-1||n.indexOf("Trident")>-1)&&(this.ie=!0)}return n(o,[{key:"log",value:function(t){var n=arguments.length>1&&void 0!==arguments[1]?arguments[1]:"debug",r=this.opt.log;this.opt.debug&&"object"===(void 0===r?"undefined":e(r))&&"function"==typeof r[n]&&r[n]("mark.js: "+t)}},{key:"escapeStr",value:function(e){return e.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g,"\\$&")}},{key:"createRegExp",value:function(e){return"disabled"!==this.opt.wildcards&&(e=this.setupWildcardsRegExp(e)),e=this.escapeStr(e),Object.keys(this.opt.synonyms).length&&(e=this.createSynonymsRegExp(e)),(this.opt.ignoreJoiners||this.opt.ignorePunctuation.length)&&(e=this.setupIgnoreJoinersRegExp(e)),this.opt.diacritics&&(e=this.createDiacriticsRegExp(e)),e=this.createMergedBlanksRegExp(e),(this.opt.ignoreJoiners||this.opt.ignorePunctuation.length)&&(e=this.createJoinersRegExp(e)),"disabled"!==this.opt.wildcards&&(e=this.createWildcardsRegExp(e)),e=this.createAccuracyRegExp(e)}},{key:"createSynonymsRegExp",value:function(e){var t=this.opt.synonyms,n=this.opt.caseSensitive?"":"i",r=this.opt.ignoreJoiners||this.opt.ignorePunctuation.length?"\0":"";for(var i in t)if(t.hasOwnProperty(i)){var o=t[i],a="disabled"!==this.opt.wildcards?this.setupWildcardsRegExp(i):this.escapeStr(i),s="disabled"!==this.opt.wildcards?this.setupWildcardsRegExp(o):this.escapeStr(o);""!==a&&""!==s&&(e=e.replace(new RegExp("("+this.escapeStr(a)+"|"+this.escapeStr(s)+")","gm"+n),r+"("+this.processSynomyms(a)+"|"+this.processSynomyms(s)+")"+r))}return e}},{key:"processSynomyms",value:function(e){return(this.opt.ignoreJoiners||this.opt.ignorePunctuation.length)&&(e=this.setupIgnoreJoinersRegExp(e)),e}},{key:"setupWildcardsRegExp",value:function(e){return(e=e.replace(/(?:\\)*\?/g,function(e){return"\\"===e.charAt(0)?"?":"
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diff --git a/index.html b/index.html
index ebb47bb..9d3a1dd 100644
--- a/index.html
+++ b/index.html
@@ -5,7 +5,6 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.">
 <title>COSMOS (Causal Oriented Search of Multi-Omic Space) • cosmosR</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
@@ -15,16 +14,14 @@
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-<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet">
+<link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
 <meta property="og:title" content="COSMOS (Causal Oriented Search of Multi-Omic Space)">
+<meta name="description" content="COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.">
 <meta property="og:description" content="COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.">
 <meta property="og:image" content="/logo.png">
-<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -34,63 +31,40 @@
 </head>
 <body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
-<li class="nav-item">
-  <a class="nav-link" href="reference/index.html">Reference</a>
-</li>
+<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="news/index.html">Changelog</a>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
+<li><a class="dropdown-item" href="articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul>
 </li>
+<li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
       </ul>
-<form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
-</form>
-
-      <ul class="navbar-nav">
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+<ul class="navbar-nav">
+<li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul>
 </div>
 
-    
+
   </div>
 </nav><div class="container template-home">
 <div class="row">
@@ -132,12 +106,12 @@ <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
 <div class="section level2">
 <h2 id="tutorial-to-use-mofa-nad-cosmos">tutorial to use MOFA nad COSMOS<a class="anchor" aria-label="anchor" href="#tutorial-to-use-mofa-nad-cosmos"></a>
 </h2>
-<p>[Here](<a href="https://saezlab.github.io/cosmosR/articles/MOFA_to_COSMOS.html" class="external-link">https://github.com/saezlab/Factor_COSMOS</a> you can find an extensive tutorial showing how to use MOFA and COSMOS with the NCI60 dataset. This is an extensive tutorial, if you wish to get a quicker plug and play introduction to COSMOS, see below.</p>
+<p><a href="https://saezlab.github.io/cosmosR/articles/MOFA_to_COSMOS.html" class="external-link">Here</a> you can find an extensive tutorial showing how to use MOFA and COSMOS with the NCI60 dataset. This is an extensive tutorial, if you wish to get a quicker plug and play introduction to COSMOS, see below.</p>
 </div>
 <div class="section level2">
 <h2 id="tutorial-nci60-playground">Tutorial (NCI60 playground)<a class="anchor" aria-label="anchor" href="#tutorial-nci60-playground"></a>
 </h2>
-<p>We made a repository that contains pre-processed inputs and an example script to use cosmos with the NCI60 RNA+metabolomic datasets. You can find the repository [here](<a href="https://saezlab.github.io/cosmosR/articles/NCI60_tutorial.html" class="external-link">https://github.com/saezlab/COSMOS_basic</a>.</p>
+<p>We made a repository that contains pre-processed inputs and an example script to use cosmos with the NCI60 RNA+metabolomic datasets. You can find the repository <a href="https://saezlab.github.io/cosmosR/articles/NCI60_tutorial.html" class="external-link">here</a>.</p>
 </div>
 <div class="section level2">
 <h2 id="access">Access<a class="anchor" aria-label="anchor" href="#access"></a>
@@ -208,15 +182,15 @@ <h2 data-toc-skip>Dev status</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer>
 </div>
 
-  
 
-  
+
+
 
   </body>
 </html>
diff --git a/katex-auto.js b/katex-auto.js
new file mode 100644
index 0000000..20651d9
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+document.addEventListener("DOMContentLoaded", function () {
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diff --git a/lightswitch.js b/lightswitch.js
new file mode 100644
index 0000000..9467125
--- /dev/null
+++ b/lightswitch.js
@@ -0,0 +1,85 @@
+
+/*!
+ * Color mode toggler for Bootstrap's docs (https://getbootstrap.com/)
+ * Copyright 2011-2023 The Bootstrap Authors
+ * Licensed under the Creative Commons Attribution 3.0 Unported License.
+ * Updates for {pkgdown} by the {bslib} authors, also licensed under CC-BY-3.0.
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+
+const getStoredTheme = () => localStorage.getItem('theme')
+const setStoredTheme = theme => localStorage.setItem('theme', theme)
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+const getPreferredTheme = () => {
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+
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+
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+setTheme(getPreferredTheme());
+bsSetupThemeToggle();
diff --git a/news/index.html b/news/index.html
index d088bbc..87a9a6c 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Changelog"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Changelog"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="active nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-news">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Changelog</h1>
-      <small>Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
+      <small>Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
     <div class="section level2">
@@ -84,14 +57,14 @@ <h2 class="pkg-version" data-toc-text="0.99.2" id="changes-in-version-0992-2020-
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/pkgdown.js b/pkgdown.js
index 9bd6621..9757bf9 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -152,5 +152,3 @@ async function searchFuse(query, callback) {
   });
   });
 })(window.jQuery || window.$)
-
-
diff --git a/pkgdown.yml b/pkgdown.yml
index ba5101e..2a31088 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,8 @@
-pandoc: 3.1.13
-pkgdown: 2.0.9
+pandoc: '3.2'
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   MOFA_to_COSMOS: MOFA_to_COSMOS.html
   NCI60_tutorial: NCI60_tutorial.html
   tutorial: tutorial.html
-last_built: 2024-06-24T08:13Z
-
+last_built: 2024-07-15T09:38Z
diff --git a/reference/HMDB_mapper_vec.html b/reference/HMDB_mapper_vec.html
index 46888dd..7694a8f 100644
--- a/reference/HMDB_mapper_vec.html
+++ b/reference/HMDB_mapper_vec.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><title>Toy Input Transcription Data Set — HMDB_mapper_vec • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Transcription Data Set — HMDB_mapper_vec"><meta property="og:description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Toy Input Transcription Data Set — HMDB_mapper_vec • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Transcription Data Set — HMDB_mapper_vec"><meta name="description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
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-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Toy Input Transcription Data Set</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/HMDB_mapper_vec.R" class="external-link"><code>R/HMDB_mapper_vec.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/HMDB_mapper_vec.R" class="external-link"><code>R/HMDB_mapper_vec.R</code></a></small>
       <div class="d-none name"><code>HMDB_mapper_vec.Rd</code></div>
     </div>
 
@@ -95,7 +68,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -104,14 +77,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
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-  
 
-  
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diff --git a/reference/compress_same_children.html b/reference/compress_same_children.html
index b1be09c..9339762 100644
--- a/reference/compress_same_children.html
+++ b/reference/compress_same_children.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function compresses a network by merging nodes that have the same children.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Compress Network by Merging Nodes with Identical Children — compress_same_children • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Compress Network by Merging Nodes with Identical Children — compress_same_children"><meta name="description" content="This function compresses a network by merging nodes that have the same children.
 The input network is represented as a data frame with three columns: source, target, and sign of interaction.
-The function returns a list containing the compressed network, node signatures, and duplicated signatures."><title>Compress Network by Merging Nodes with Identical Children — compress_same_children • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Compress Network by Merging Nodes with Identical Children — compress_same_children"><meta property="og:description" content="This function compresses a network by merging nodes that have the same children.
+The function returns a list containing the compressed network, node signatures, and duplicated signatures."><meta property="og:description" content="This function compresses a network by merging nodes that have the same children.
 The input network is represented as a data frame with three columns: source, target, and sign of interaction.
-The function returns a list containing the compressed network, node signatures, and duplicated signatures."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+The function returns a list containing the compressed network, node signatures, and duplicated signatures."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -14,64 +11,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://saezlab.org">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Compress Network by Merging Nodes with Identical Children</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/compress_same_children.R" class="external-link"><code>R/compress_same_children.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/compress_same_children.R" class="external-link"><code>R/compress_same_children.R</code></a></small>
       <div class="d-none name"><code>compress_same_children.Rd</code></div>
     </div>
 
@@ -88,23 +61,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>df</dt>
+
+
+<dl><dt id="arg-df">df<a class="anchor" aria-label="anchor" href="#arg-df"></a></dt>
 <dd><p>A data frame representing the network with three columns: source, target, and sign of interaction.</p></dd>
 
 
-<dt>sig_input</dt>
+<dt id="arg-sig-input">sig_input<a class="anchor" aria-label="anchor" href="#arg-sig-input"></a></dt>
 <dd><p>A list of input node signatures to be considered for the merging process.</p></dd>
 
 
-<dt>metab_input</dt>
+<dt id="arg-metab-input">metab_input<a class="anchor" aria-label="anchor" href="#arg-metab-input"></a></dt>
 <dd><p>A list of input metabolic signatures to be considered for the merging process.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list containing the following elements:</p>
+    <p>A list containing the following elements:</p>
 <dl><dt>compressed_network</dt>
 <dd><p>A data frame representing the compressed network.</p></dd>
 
@@ -133,7 +106,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -142,14 +115,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/cosmos_data.html b/reference/cosmos_data.html
index a7160c4..ca019a5 100644
--- a/reference/cosmos_data.html
+++ b/reference/cosmos_data.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="An S3 class that combines the required data into a comprehensive list.  Use 
-the preprocess_COSMOS_signaling_to_metabolism or 
-preprocess_COSMOS_metabolism_to_signaling to create an instance."><title>Create Cosmos Data — cosmos_data • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Cosmos Data — cosmos_data"><meta property="og:description" content="An S3 class that combines the required data into a comprehensive list.  Use 
-the preprocess_COSMOS_signaling_to_metabolism or 
-preprocess_COSMOS_metabolism_to_signaling to create an instance."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create Cosmos Data — cosmos_data • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Cosmos Data — cosmos_data"><meta name="description" content="An S3 class that combines the required data into a comprehensive list.  Use
+the preprocess_COSMOS_signaling_to_metabolism or
+preprocess_COSMOS_metabolism_to_signaling to create an instance."><meta property="og:description" content="An S3 class that combines the required data into a comprehensive list.  Use
+the preprocess_COSMOS_signaling_to_metabolism or
+preprocess_COSMOS_metabolism_to_signaling to create an instance."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,70 +11,46 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Create Cosmos Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/cosmos_data.R" class="external-link"><code>R/cosmos_data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/cosmos_data.R" class="external-link"><code>R/cosmos_data.R</code></a></small>
       <div class="d-none name"><code>cosmos_data.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>An S3 class that combines the required data into a comprehensive list.  Use 
-the <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> or 
+    <p>An S3 class that combines the required data into a comprehensive list.  Use
+the <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> or
 <code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> to create an instance.</p>
     </div>
 
@@ -95,52 +68,52 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>meta_network</dt>
+
+
+<dl><dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>Prior knowledge network (PKN).  By default COSMOS use a
-PKN derived from Omnipath, STITCHdb and Recon3D.  See details on the data 
+PKN derived from Omnipath, STITCHdb and Recon3D.  See details on the data
 <code><a href="meta_network.html">meta_network</a></code>.</p></dd>
 
 
-<dt>tf_regulon</dt>
+<dt id="arg-tf-regulon">tf_regulon<a class="anchor" aria-label="anchor" href="#arg-tf-regulon"></a></dt>
 <dd><p>Collection of transcription factor - target interactions.
-A default collection from dorothea can be obtained by the 
+A default collection from dorothea can be obtained by the
 <code><a href="load_tf_regulon_dorothea.html">load_tf_regulon_dorothea</a></code> function.</p></dd>
 
 
-<dt>signaling_data</dt>
-<dd><p>Numerical vector, where names are signaling nodes 
-in the PKN and values are from {1, 0, -1}.  Continuous data will be 
+<dt id="arg-signaling-data">signaling_data<a class="anchor" aria-label="anchor" href="#arg-signaling-data"></a></dt>
+<dd><p>Numerical vector, where names are signaling nodes
+in the PKN and values are from {1, 0, -1}.  Continuous data will be
 discretized using the <code><a href="https://rdrr.io/r/base/sign.html" class="external-link">sign</a></code> function.</p></dd>
 
 
-<dt>metabolic_data</dt>
-<dd><p>Numerical vector, where names are metabolic nodes 
-in the PKN and values are continuous values that represents log2 fold change 
-or t-values from a differential analysis.  These values are compared to 
+<dt id="arg-metabolic-data">metabolic_data<a class="anchor" aria-label="anchor" href="#arg-metabolic-data"></a></dt>
+<dd><p>Numerical vector, where names are metabolic nodes
+in the PKN and values are continuous values that represents log2 fold change
+or t-values from a differential analysis.  These values are compared to
 the simulation results (simulated nodes can take value -1, 0 or 1).</p></dd>
 
 
-<dt>expression_data</dt>
-<dd><p>Numerical vector that represents the results of a 
-differential gene expression analysis. Names are gene names using EntrezID 
-starting with an X and values are log fold change or t-values. Genes with 
+<dt id="arg-expression-data">expression_data<a class="anchor" aria-label="anchor" href="#arg-expression-data"></a></dt>
+<dd><p>Numerical vector that represents the results of a
+differential gene expression analysis. Names are gene names using EntrezID
+starting with an X and values are log fold change or t-values. Genes with
 NA values are considered none expressed and they will be removed from the
 TF-gene expression interactions.</p></dd>
 
 
-<dt>verbose</dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
 <dd><p>(default: TRUE) Reports details about the
 <code>cosmos_data</code> object.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p><code>cosmos data</code> class instance.</p>
+    <p><code>cosmos data</code> class instance.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -149,14 +122,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/createLinearColors.html b/reference/createLinearColors.html
index afc7ea2..09ae12d 100644
--- a/reference/createLinearColors.html
+++ b/reference/createLinearColors.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function generates a gradient of colors based on the provided numeric values. The colors can be adjusted to include zero and are configurable with a specified maximum and custom color palette."><title>Create Linear Colors Based on Numeric Input — createLinearColors • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Linear Colors Based on Numeric Input — createLinearColors"><meta property="og:description" content="This function generates a gradient of colors based on the provided numeric values. The colors can be adjusted to include zero and are configurable with a specified maximum and custom color palette."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create Linear Colors Based on Numeric Input — createLinearColors • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Linear Colors Based on Numeric Input — createLinearColors"><meta name="description" content="This function generates a gradient of colors based on the provided numeric values. The colors can be adjusted to include zero and are configurable with a specified maximum and custom color palette."><meta property="og:description" content="This function generates a gradient of colors based on the provided numeric values. The colors can be adjusted to include zero and are configurable with a specified maximum and custom color palette."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Create Linear Colors Based on Numeric Input</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_pheatmap.R" class="external-link"><code>R/support_pheatmap.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_pheatmap.R" class="external-link"><code>R/support_pheatmap.R</code></a></small>
       <div class="d-none name"><code>createLinearColors.Rd</code></div>
     </div>
 
@@ -87,27 +60,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>numbers</dt>
+
+
+<dl><dt id="arg-numbers">numbers<a class="anchor" aria-label="anchor" href="#arg-numbers"></a></dt>
 <dd><p>A numeric vector for which the color gradient is to be generated.</p></dd>
 
 
-<dt>withZero</dt>
+<dt id="arg-withzero">withZero<a class="anchor" aria-label="anchor" href="#arg-withzero"></a></dt>
 <dd><p>A logical value indicating whether zero should be included in the color gradient. Default is TRUE.</p></dd>
 
 
-<dt>maximum</dt>
+<dt id="arg-maximum">maximum<a class="anchor" aria-label="anchor" href="#arg-maximum"></a></dt>
 <dd><p>An integer specifying the maximum number of colors to be generated in the gradient. Default is 100.</p></dd>
 
 
-<dt>my_colors</dt>
+<dt id="arg-my-colors">my_colors<a class="anchor" aria-label="anchor" href="#arg-my-colors"></a></dt>
 <dd><p>A character vector of length three specifying the colors to be used in the gradient. Default is c("royalblue3", "white", "red").</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A character vector of colors representing the gradient based on the input numeric values.</p>
+    <p>A character vector of colors representing the gradient based on the input numeric values.</p>
     </div>
 
     <div class="section level2">
@@ -118,7 +91,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -127,14 +100,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/decompress_moon_result.html b/reference/decompress_moon_result.html
index 50eaf95..f977eef 100644
--- a/reference/decompress_moon_result.html
+++ b/reference/decompress_moon_result.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function decompresses the results obtained from moon analysis by incorporating 
-node signatures and handling duplicated parents. It merges these details with the 
-provided meta network data and returns a comprehensive data frame."><title>Decompress Moon Result — decompress_moon_result • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Decompress Moon Result — decompress_moon_result"><meta property="og:description" content="This function decompresses the results obtained from moon analysis by incorporating 
-node signatures and handling duplicated parents. It merges these details with the 
-provided meta network data and returns a comprehensive data frame."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Decompress Moon Result — decompress_moon_result • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Decompress Moon Result — decompress_moon_result"><meta name="description" content="This function decompresses the results obtained from moon analysis by incorporating
+node signatures and handling duplicated parents. It merges these details with the
+provided meta network data and returns a comprehensive data frame."><meta property="og:description" content="This function decompresses the results obtained from moon analysis by incorporating
+node signatures and handling duplicated parents. It merges these details with the
+provided meta network data and returns a comprehensive data frame."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,70 +11,46 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Decompress Moon Result</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>decompress_moon_result.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function decompresses the results obtained from moon analysis by incorporating 
-node signatures and handling duplicated parents. It merges these details with the 
+    <p>This function decompresses the results obtained from moon analysis by incorporating
+node signatures and handling duplicated parents. It merges these details with the
 provided meta network data and returns a comprehensive data frame.</p>
     </div>
 
@@ -88,24 +61,24 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>moon_res</dt>
+
+
+<dl><dt id="arg-moon-res">moon_res<a class="anchor" aria-label="anchor" href="#arg-moon-res"></a></dt>
 <dd><p>A data frame containing the results of a moon analysis.</p></dd>
 
 
-<dt>meta_network_compressed_list</dt>
-<dd><p>A list containing compressed meta network details, 
+<dt id="arg-meta-network-compressed-list">meta_network_compressed_list<a class="anchor" aria-label="anchor" href="#arg-meta-network-compressed-list"></a></dt>
+<dd><p>A list containing compressed meta network details,
 including node signatures and duplicated parents.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A data frame representing the original meta network.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame which merges the moon analysis results with the meta network data,
+    <p>A data frame which merges the moon analysis results with the meta network data,
         including additional details about node signatures and handling of duplicated parents.</p>
     </div>
 
@@ -118,7 +91,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -127,14 +100,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/decompress_solution_network.html b/reference/decompress_solution_network.html
index becd1f6..2757cd5 100644
--- a/reference/decompress_solution_network.html
+++ b/reference/decompress_solution_network.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function decompresses a solution network by mapping node signatures back to their original identifiers.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Decompress Solution Network — decompress_solution_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Decompress Solution Network — decompress_solution_network"><meta name="description" content="This function decompresses a solution network by mapping node signatures back to their original identifiers.
 The input is a formatted solution network, a meta network, node signatures, and duplicated parents.
-The function returns a list containing the decompressed solution network and attribute table."><title>Decompress Solution Network — decompress_solution_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Decompress Solution Network — decompress_solution_network"><meta property="og:description" content="This function decompresses a solution network by mapping node signatures back to their original identifiers.
+The function returns a list containing the decompressed solution network and attribute table."><meta property="og:description" content="This function decompresses a solution network by mapping node signatures back to their original identifiers.
 The input is a formatted solution network, a meta network, node signatures, and duplicated parents.
-The function returns a list containing the decompressed solution network and attribute table."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+The function returns a list containing the decompressed solution network and attribute table."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,64 +11,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Decompress Solution Network</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/compress_same_children.R" class="external-link"><code>R/compress_same_children.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/compress_same_children.R" class="external-link"><code>R/compress_same_children.R</code></a></small>
       <div class="d-none name"><code>decompress_solution_network.Rd</code></div>
     </div>
 
@@ -93,27 +66,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>formatted_res</dt>
+
+
+<dl><dt id="arg-formatted-res">formatted_res<a class="anchor" aria-label="anchor" href="#arg-formatted-res"></a></dt>
 <dd><p>A list containing the solution network and attribute table.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A data frame representing the meta network.</p></dd>
 
 
-<dt>node_signatures</dt>
+<dt id="arg-node-signatures">node_signatures<a class="anchor" aria-label="anchor" href="#arg-node-signatures"></a></dt>
 <dd><p>A list of node signatures.</p></dd>
 
 
-<dt>duplicated_parents</dt>
+<dt id="arg-duplicated-parents">duplicated_parents<a class="anchor" aria-label="anchor" href="#arg-duplicated-parents"></a></dt>
 <dd><p>A list of duplicated parents from the compression process.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list containing the following elements:</p>
+    <p>A list containing the following elements:</p>
 <dl><dt>SIF</dt>
 <dd><p>A data frame representing the decompressed solution network.</p></dd>
 
@@ -156,7 +129,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -165,14 +138,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/decoupleRnival.html b/reference/decoupleRnival.html
index 0b52cf0..60b1ab2 100644
--- a/reference/decoupleRnival.html
+++ b/reference/decoupleRnival.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Iteratively propagate downstream input activity through a signed directed network
-using the weighted mean enrichment score from decoupleR package"><title>DecoupleRnival — decoupleRnival • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="DecoupleRnival — decoupleRnival"><meta property="og:description" content="Iteratively propagate downstream input activity through a signed directed network
-using the weighted mean enrichment score from decoupleR package"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>DecoupleRnival — decoupleRnival • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="DecoupleRnival — decoupleRnival"><meta name="description" content="Iteratively propagate downstream input activity through a signed directed network
+using the weighted mean enrichment score from decoupleR package"><meta property="og:description" content="Iteratively propagate downstream input activity through a signed directed network
+using the weighted mean enrichment score from decoupleR package"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
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-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>DecoupleRnival</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>decoupleRnival.Rd</code></div>
     </div>
 
@@ -93,39 +66,39 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>upstream_input</dt>
+
+
+<dl><dt id="arg-upstream-input">upstream_input<a class="anchor" aria-label="anchor" href="#arg-upstream-input"></a></dt>
 <dd><p>A named vector with up_stream nodes and their corresponding activity.</p></dd>
 
 
-<dt>downstream_input</dt>
+<dt id="arg-downstream-input">downstream_input<a class="anchor" aria-label="anchor" href="#arg-downstream-input"></a></dt>
 <dd><p>A named vector with down_stream nodes and their corresponding activity.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A network data frame containing signed directed prior knowledge of molecular interactions.</p></dd>
 
 
-<dt>n_layers</dt>
+<dt id="arg-n-layers">n_layers<a class="anchor" aria-label="anchor" href="#arg-n-layers"></a></dt>
 <dd><p>The number of layers that will be propagated upstream.</p></dd>
 
 
-<dt>n_perm</dt>
+<dt id="arg-n-perm">n_perm<a class="anchor" aria-label="anchor" href="#arg-n-perm"></a></dt>
 <dd><p>The number of permutations to use in decoupleR's algorithm.</p></dd>
 
 
-<dt>downstream_cutoff</dt>
+<dt id="arg-downstream-cutoff">downstream_cutoff<a class="anchor" aria-label="anchor" href="#arg-downstream-cutoff"></a></dt>
 <dd><p>If downstream measurments should be included above a given threshold</p></dd>
 
 
-<dt>statistic</dt>
+<dt id="arg-statistic">statistic<a class="anchor" aria-label="anchor" href="#arg-statistic"></a></dt>
 <dd><p>the decoupleR stat to consider: "wmean", "norm_wmean", or "ulm"</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame containing the score of the nodes upstream of the 
+    <p>A data frame containing the score of the nodes upstream of the
 downstream input based on the iterative propagation</p>
     </div>
 
@@ -153,7 +126,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> E      E -1.50000</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -162,14 +135,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/default_CARNIVAL_options.html b/reference/default_CARNIVAL_options.html
index 5e395a4..284fa2f 100644
--- a/reference/default_CARNIVAL_options.html
+++ b/reference/default_CARNIVAL_options.html
@@ -1,16 +1,13 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the default CARNIVAL options as a list.  You can modify the elements
-of the list and then use it as an argument in run_COSMOS_metabolism_to_signaling or 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Setting Default CARNIVAL Options — default_CARNIVAL_options • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Setting Default CARNIVAL Options — default_CARNIVAL_options"><meta name="description" content="Returns the default CARNIVAL options as a list.  You can modify the elements
+of the list and then use it as an argument in run_COSMOS_metabolism_to_signaling or
  run_COSMOS_signaling_to_metabolism.
-If you choose CPLEX or CBC, you must modify then the solverPath field and point to 
-the CPLEX/CBC executable (See Details)."><title>Setting Default CARNIVAL Options — default_CARNIVAL_options • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Setting Default CARNIVAL Options — default_CARNIVAL_options"><meta property="og:description" content="Returns the default CARNIVAL options as a list.  You can modify the elements
-of the list and then use it as an argument in run_COSMOS_metabolism_to_signaling or 
+If you choose CPLEX or CBC, you must modify then the solverPath field and point to
+the CPLEX/CBC executable (See Details)."><meta property="og:description" content="Returns the default CARNIVAL options as a list.  You can modify the elements
+of the list and then use it as an argument in run_COSMOS_metabolism_to_signaling or
  run_COSMOS_signaling_to_metabolism.
-If you choose CPLEX or CBC, you must modify then the solverPath field and point to 
-the CPLEX/CBC executable (See Details)."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+If you choose CPLEX or CBC, you must modify then the solverPath field and point to
+the CPLEX/CBC executable (See Details)."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -18,72 +15,48 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Setting Default CARNIVAL Options</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/default_CARNIVAL_options.R" class="external-link"><code>R/default_CARNIVAL_options.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/default_CARNIVAL_options.R" class="external-link"><code>R/default_CARNIVAL_options.R</code></a></small>
       <div class="d-none name"><code>default_CARNIVAL_options.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Returns the default CARNIVAL options as a list.  You can modify the elements
-of the list and then use it as an argument in <code><a href="run_COSMOS_metabolism_to_signaling.html">run_COSMOS_metabolism_to_signaling</a></code> or 
+of the list and then use it as an argument in <code><a href="run_COSMOS_metabolism_to_signaling.html">run_COSMOS_metabolism_to_signaling</a></code> or
  <code><a href="run_COSMOS_signaling_to_metabolism.html">run_COSMOS_signaling_to_metabolism</a></code>.
-If you choose CPLEX or CBC, you must modify then the solverPath field and point to 
+If you choose CPLEX or CBC, you must modify then the solverPath field and point to
 the CPLEX/CBC executable (See Details).</p>
     </div>
 
@@ -94,15 +67,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>solver</dt>
+
+
+<dl><dt id="arg-solver">solver<a class="anchor" aria-label="anchor" href="#arg-solver"></a></dt>
 <dd><p>one of `cplex` (recommended, but require 3rd party tool), `cbc` (also require 3rd party tool) or `lpSolve` (only for small networks)</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>returns a list with all possible options implemented in CARNIVAL.
+    <p>returns a list with all possible options implemented in CARNIVAL.
 see the documentation on <code><a href="https://rdrr.io/pkg/CARNIVAL/man/runCARNIVAL.html" class="external-link">runCARNIVAL</a></code>.</p>
     </div>
     <div class="section level2">
@@ -114,10 +87,10 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 Gurobi license is also free for academics, request a license following instructions
 <a href="https://www.gurobi.com/downloads/end-user-license-agreement-academic/" class="external-link">here</a>.
 The  <a href="https://projects.coin-or.org/Cbc" class="external-link">CBC</a> solver is open source and freely
-available for any user, but has a significantly lower performance than CPLEX or 
+available for any user, but has a significantly lower performance than CPLEX or
 Gurobi. Obtain CBC executable directly usable for cosmos
 <a href="https://ampl.com/products/solvers/open-source/#cbc" class="external-link">here</a>. Alternatively for
-small networks, users can rely on the freely available 
+small networks, users can rely on the freely available
  <a href="https://cran.r-project.org/web/packages/lpSolve/index.html" class="external-link">lpSolve R-package</a>,
  which is automatically installed with the package.</p>
     </div>
@@ -132,7 +105,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">my_options</span><span class="op">$</span><span class="va">timelimit</span> <span class="op">=</span> <span class="fl">3600</span><span class="op">*</span><span class="fl">15</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -141,14 +114,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/display_node_neighboorhood.html b/reference/display_node_neighboorhood.html
index f8f90da..778492b 100644
--- a/reference/display_node_neighboorhood.html
+++ b/reference/display_node_neighboorhood.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="display input and measurements within n steps of a given set of nodes"><title>display_node_neighboorhood — display_node_neighboorhood • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="display_node_neighboorhood — display_node_neighboorhood"><meta property="og:description" content="display input and measurements within n steps of a given set of nodes"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>display_node_neighboorhood — display_node_neighboorhood • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="display_node_neighboorhood — display_node_neighboorhood"><meta name="description" content="display input and measurements within n steps of a given set of nodes"><meta property="og:description" content="display input and measurements within n steps of a given set of nodes"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -10,64 +7,40 @@
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 </script><!-- dependencies from examples --><script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script><link href="libs/vis-9.1.0/vis-network.min.css" rel="stylesheet"><script src="libs/vis-9.1.0/vis-network.min.js"></script><script src="libs/visNetwork-binding-2.1.2/visNetwork.js"></script></head><body>
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
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 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>display_node_neighboorhood</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/display_node_neighboorhood.R" class="external-link"><code>R/display_node_neighboorhood.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/display_node_neighboorhood.R" class="external-link"><code>R/display_node_neighboorhood.R</code></a></small>
       <div class="d-none name"><code>display_node_neighboorhood.Rd</code></div>
     </div>
 
@@ -82,31 +55,31 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>central_node</dt>
-<dd><p>character or character vector; node ID(s) around which a 
+
+
+<dl><dt id="arg-central-node">central_node<a class="anchor" aria-label="anchor" href="#arg-central-node"></a></dt>
+<dd><p>character or character vector; node ID(s) around which a
 network will be branched out untill meansurments and input are reached</p></dd>
 
 
-<dt>sif</dt>
+<dt id="arg-sif">sif<a class="anchor" aria-label="anchor" href="#arg-sif"></a></dt>
 <dd><p>df; COSMOS network solution in sif format like the first list
 element returned by the format_cosmos_res function</p></dd>
 
 
-<dt>att</dt>
-<dd><p>df; attributes of the nodes of the COMSOS network solution like 
+<dt id="arg-att">att<a class="anchor" aria-label="anchor" href="#arg-att"></a></dt>
+<dd><p>df; attributes of the nodes of the COMSOS network solution like
 the second list element returned by the format_cosmos_res function</p></dd>
 
 
-<dt>n</dt>
-<dd><p>numeric; maximum number of steps in the network to look for inputs 
+<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
+<dd><p>numeric; maximum number of steps in the network to look for inputs
 and measurments</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>a visnetwork object</p>
+    <p>a visnetwork object</p>
     </div>
 
     <div class="section level2">
@@ -139,16 +112,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_33d24_06_2024n45.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_30d15_07_2024n45.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_33d24_06_2024n45.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:33 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_30d15_07_2024n45.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:30 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -158,14 +131,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -179,16 +152,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign().</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_34d24_06_2024n23.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_31d15_07_2024n23.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_34d24_06_2024n23.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_31d15_07_2024n23.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -198,14 +171,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:34 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:31 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-in"><span><span class="va">test_result_for</span> <span class="op">&lt;-</span> <span class="fu"><a href="format_COSMOS_res.html">format_COSMOS_res</a></span><span class="op">(</span><span class="va">test_result_for</span><span class="op">)</span></span></span>
@@ -218,7 +191,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <div id="htmlwidget-ac96cb3ee4656e2e9ec3" style="width:1600px;height:1600px;" class="visNetwork html-widget"></div>
 <script type="application/json" data-for="htmlwidget-ac96cb3ee4656e2e9ec3">{"x":{"nodes":{"id":["Enzyme1338__AKR1A1","Enzyme7338__LDHB_LDHA_reverse","Enzyme9049__SLC2A1_reverse","FGFR1","LDHA","MAPK14","MYC","Metab__D-Glucitol_c","Metab__D-Glucose_c","Metab__L-Lactic acid_c","SLC2A1"],"NodeType":["","","","","","","P","M","","M",""],"ZeroAct":[0,0,0,0,0,0,0,0,0,0,0],"UpAct":[1,1,1,1,1,1,1,1,1,1,1],"DownAct":[0,0,0,0,0,0,0,0,0,0,0],"AvgAct":[1,1,1,1,1,1,1,1,1,1,1],"measured":[0,0,0,0,0,0,1,1,0,1,0],"Activity":[1,1,1,1,1,1,1,1,1,1,1],"label":["Enzyme1338__AKR1A1","Enzyme7338__LDHB_LDHA_reverse","Enzyme9049__SLC2A1_reverse","FGFR1","LDHA","MAPK14","MYC","Metab__D-Glucitol_c","Metab__D-Glucose_c","Metab__L-Lactic acid_c","SLC2A1"],"color":["green","green","green","green","green","green","green","green","green","green","green"],"shape":["dot","dot","dot","dot","dot","dot","dot","dot","dot","dot","dot"],"shadow":[false,false,false,false,false,false,true,true,false,true,false]},"edges":{"from":["MAPK14","Metab__D-Glucitol_c","FGFR1","Enzyme1338__AKR1A1","Enzyme7338__LDHB_LDHA_reverse","Enzyme9049__SLC2A1_reverse","LDHA","MAPK14","MYC","Metab__D-Glucose_c","SLC2A1"],"to":["MYC","MAPK14","LDHA","Metab__D-Glucitol_c","Metab__L-Lactic acid_c","Metab__D-Glucose_c","Enzyme7338__LDHB_LDHA_reverse","FGFR1","SLC2A1","Enzyme1338__AKR1A1","Enzyme9049__SLC2A1_reverse"],"sign":[1,1,1,1,1,1,1,-1,1,1,1],"weigth":[1,1,1,1,1,1,1,0,1,1,1],"color":["grey","grey","grey","grey","grey","grey","grey","grey","grey","grey","grey"],"arrows.to.type":["arrow","arrow","arrow","arrow","arrow","arrow","arrow","circle","arrow","arrow","arrow"],"enabled":[true,true,true,true,true,true,true,true,true,true,true],"scaleFactor":[1,1,1,1,1,1,1,1,1,1,1]},"nodesToDataframe":true,"edgesToDataframe":true,"options":{"width":"100%","height":"100%","nodes":{"shape":"dot"},"manipulation":{"enabled":false}},"groups":null,"width":1600,"height":1600,"idselection":{"enabled":true,"style":"width: 200px; height: 26px;\n                                              background: #f8f8f8;\n                                              color: darkblue;\n                                              border:none;\n                                              outline:none;","useLabels":true,"main":"Select by id"},"byselection":{"enabled":false,"style":"width: 150px; height: 26px","multiple":false,"hideColor":"rgba(200,200,200,0.5)","highlight":false},"main":null,"submain":null,"footer":null,"background":"rgba(0, 0, 0, 0)","highlight":{"enabled":true,"hoverNearest":false,"degree":1,"algorithm":"all","hideColor":"rgba(200,200,200,0.5)","labelOnly":true},"collapse":{"enabled":false,"fit":false,"resetHighlight":true,"clusterOptions":null,"keepCoord":true,"labelSuffix":"(cluster)"}},"evals":[],"jsHooks":[]}</script></code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -227,14 +200,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
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diff --git a/reference/extract_nodes_for_ORA.html b/reference/extract_nodes_for_ORA.html
index 7c1cf8f..6e19604 100644
--- a/reference/extract_nodes_for_ORA.html
+++ b/reference/extract_nodes_for_ORA.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function to extract the nodes that appear in the COSMOS output network and
-the background genes (all genes present in the prior knowledge network)"><title>Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA"><meta property="og:description" content="Function to extract the nodes that appear in the COSMOS output network and
-the background genes (all genes present in the prior knowledge network)"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA"><meta name="description" content="Function to extract the nodes that appear in the COSMOS output network and
+the background genes (all genes present in the prior knowledge network)"><meta property="og:description" content="Function to extract the nodes that appear in the COSMOS output network and
+the background genes (all genes present in the prior knowledge network)"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -12,64 +9,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Extract COSMOS nodes for ORA analysis</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_ORA.R" class="external-link"><code>R/support_ORA.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_ORA.R" class="external-link"><code>R/support_ORA.R</code></a></small>
       <div class="d-none name"><code>extract_nodes_for_ORA.Rd</code></div>
     </div>
 
@@ -85,21 +58,21 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>sif</dt>
+
+
+<dl><dt id="arg-sif">sif<a class="anchor" aria-label="anchor" href="#arg-sif"></a></dt>
 <dd><p>df; COSMOS network solution in sif format like the first list
 element returned by the format_cosmos_res function</p></dd>
 
 
-<dt>att</dt>
-<dd><p>df; attributes of the nodes of the COMSOS network solution like 
+<dt id="arg-att">att<a class="anchor" aria-label="anchor" href="#arg-att"></a></dt>
+<dd><p>df; attributes of the nodes of the COMSOS network solution like
 the second list element returned by the format_cosmos_res function</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List with 2 objects: the success and the background genes</p>
+    <p>List with 2 objects: the success and the background genes</p>
     </div>
 
     <div class="section level2">
@@ -132,16 +105,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_35d24_06_2024n76.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_32d15_07_2024n76.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_35d24_06_2024n76.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_32d15_07_2024n76.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -151,14 +124,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -172,16 +145,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign().</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_35d24_06_2024n63.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_32d15_07_2024n63.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_35d24_06_2024n63.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:35 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_32d15_07_2024n63.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:32 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -191,14 +164,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:36 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:33 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-in"><span><span class="va">test_result_for</span> <span class="op">&lt;-</span> <span class="fu"><a href="format_COSMOS_res.html">format_COSMOS_res</a></span><span class="op">(</span><span class="va">test_result_for</span><span class="op">)</span></span></span>
@@ -208,7 +181,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">)</span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -217,14 +190,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/filter_incohrent_TF_target.html b/reference/filter_incohrent_TF_target.html
index b2c2ad4..9acc4d6 100644
--- a/reference/filter_incohrent_TF_target.html
+++ b/reference/filter_incohrent_TF_target.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Filters incoherent target genes from a regulatory network based on a decoupling analysis
-of upstream and downstream gene expression."><title>filter_incohrent_TF_target — filter_incohrent_TF_target • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="filter_incohrent_TF_target — filter_incohrent_TF_target"><meta property="og:description" content="Filters incoherent target genes from a regulatory network based on a decoupling analysis
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>filter_incohrent_TF_target — filter_incohrent_TF_target • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="filter_incohrent_TF_target — filter_incohrent_TF_target"><meta name="description" content="Filters incoherent target genes from a regulatory network based on a decoupling analysis
+of upstream and downstream gene expression."><meta property="og:description" content="Filters incoherent target genes from a regulatory network based on a decoupling analysis
+of upstream and downstream gene expression."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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@@ -12,64 +9,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-  <a class="external-link nav-link" href="https://saezlab.org">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>filter_incohrent_TF_target</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>filter_incohrent_TF_target.Rd</code></div>
     </div>
 
@@ -90,27 +63,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>decouplRnival_res</dt>
+
+
+<dl><dt id="arg-decouplrnival-res">decouplRnival_res<a class="anchor" aria-label="anchor" href="#arg-decouplrnival-res"></a></dt>
 <dd><p>A data frame resulting from the decoupleRnival function.</p></dd>
 
 
-<dt>TF_reg_net</dt>
+<dt id="arg-tf-reg-net">TF_reg_net<a class="anchor" aria-label="anchor" href="#arg-tf-reg-net"></a></dt>
 <dd><p>A data frame containing prior knowledge of transcription factor (TF) regulatory interactions.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A network data frame containing signed directed prior knowledge of molecular interactions.</p></dd>
 
 
-<dt>RNA_input</dt>
+<dt id="arg-rna-input">RNA_input<a class="anchor" aria-label="anchor" href="#arg-rna-input"></a></dt>
 <dd><p>A named vector containing differential gene expression data.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A network data frame containing the genes that are not incoherently regulated by TFs.</p>
+    <p>A network data frame containing the genes that are not incoherently regulated by TFs.</p>
     </div>
 
     <div class="section level2">
@@ -147,7 +120,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 7      E      A           1</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -156,14 +129,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/format_COSMOS_res.html b/reference/format_COSMOS_res.html
index 70b0442..58c9a10 100644
--- a/reference/format_COSMOS_res.html
+++ b/reference/format_COSMOS_res.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="formats the network with readable names"><title>format_COSMOS_res — format_COSMOS_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="format_COSMOS_res — format_COSMOS_res"><meta property="og:description" content="formats the network with readable names"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>format_COSMOS_res — format_COSMOS_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="format_COSMOS_res — format_COSMOS_res"><meta name="description" content="formats the network with readable names"><meta property="og:description" content="formats the network with readable names"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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@@ -10,64 +7,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
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   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>format_COSMOS_res</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/format_COSMOS_results.R" class="external-link"><code>R/format_COSMOS_results.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/format_COSMOS_results.R" class="external-link"><code>R/format_COSMOS_results.R</code></a></small>
       <div class="d-none name"><code>format_COSMOS_res.Rd</code></div>
     </div>
 
@@ -82,22 +55,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>cosmos_res</dt>
+
+
+<dl><dt id="arg-cosmos-res">cosmos_res<a class="anchor" aria-label="anchor" href="#arg-cosmos-res"></a></dt>
 <dd><p>results of COSMOS run</p></dd>
 
 
-<dt>metab_mapping</dt>
+<dt id="arg-metab-mapping">metab_mapping<a class="anchor" aria-label="anchor" href="#arg-metab-mapping"></a></dt>
 <dd><p>a named vector with HMDB Ids as names and desired metabolite names as values.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>list with network and attribute tables.</p>
+    <p>list with network and attribute tables.</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -106,14 +79,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/format_LR_ressource.html b/reference/format_LR_ressource.html
index 8d82b77..721e813 100644
--- a/reference/format_LR_ressource.html
+++ b/reference/format_LR_ressource.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function formats a ligand-receptor resource by creating a gene set
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Format Ligand-Receptor Resource — format_LR_ressource • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Format Ligand-Receptor Resource — format_LR_ressource"><meta name="description" content="This function formats a ligand-receptor resource by creating a gene set
 with source-target pairs, converting it to a long format, and adding
-default values for 'mor' and 'likelihood'."><title>Format Ligand-Receptor Resource — format_LR_ressource • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Format Ligand-Receptor Resource — format_LR_ressource"><meta property="og:description" content="This function formats a ligand-receptor resource by creating a gene set
+default values for 'mor' and 'likelihood'."><meta property="og:description" content="This function formats a ligand-receptor resource by creating a gene set
 with source-target pairs, converting it to a long format, and adding
-default values for 'mor' and 'likelihood'."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+default values for 'mor' and 'likelihood'."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,64 +11,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
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-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Format Ligand-Receptor Resource</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
       <div class="d-none name"><code>format_LR_ressource.Rd</code></div>
     </div>
 
@@ -88,15 +61,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ligrec_ressource</dt>
+
+
+<dl><dt id="arg-ligrec-ressource">ligrec_ressource<a class="anchor" aria-label="anchor" href="#arg-ligrec-ressource"></a></dt>
 <dd><p>A data frame representing the ligand-receptor resource with columns for source and target gene symbols.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame containing the formatted ligand-receptor gene set with columns:</p>
+    <p>A data frame containing the formatted ligand-receptor gene set with columns:</p>
 <dl><dt>gene</dt>
 <dd><p>The gene symbol from the ligand-receptor pairs.</p></dd>
 
@@ -122,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -131,14 +104,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/get_moon_scoring_network.html b/reference/get_moon_scoring_network.html
index ba379cb..58140b9 100644
--- a/reference/get_moon_scoring_network.html
+++ b/reference/get_moon_scoring_network.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function analyzes a given meta network based on moon scores and an upstream node. 
-It filters and processes the network by controlling and observing neighbours 
-according to specified parameters. The function returns a list containing a filtered 
-network and updated moon scores."><title>Get Moon Scoring Network — get_moon_scoring_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Get Moon Scoring Network — get_moon_scoring_network"><meta property="og:description" content="This function analyzes a given meta network based on moon scores and an upstream node. 
-It filters and processes the network by controlling and observing neighbours 
-according to specified parameters. The function returns a list containing a filtered 
-network and updated moon scores."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get Moon Scoring Network — get_moon_scoring_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Get Moon Scoring Network — get_moon_scoring_network"><meta name="description" content="This function analyzes a given meta network based on moon scores and an upstream node.
+It filters and processes the network by controlling and observing neighbours
+according to specified parameters. The function returns a list containing a filtered
+network and updated moon scores."><meta property="og:description" content="This function analyzes a given meta network based on moon scores and an upstream node.
+It filters and processes the network by controlling and observing neighbours
+according to specified parameters. The function returns a list containing a filtered
+network and updated moon scores."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,71 +13,47 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
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-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
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-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
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-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Get Moon Scoring Network</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>get_moon_scoring_network.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This function analyzes a given meta network based on moon scores and an upstream node. 
-It filters and processes the network by controlling and observing neighbours 
-according to specified parameters. The function returns a list containing a filtered 
+    <p>This function analyzes a given meta network based on moon scores and an upstream node.
+It filters and processes the network by controlling and observing neighbours
+according to specified parameters. The function returns a list containing a filtered
 network and updated moon scores.</p>
     </div>
 
@@ -96,27 +69,27 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>upstream_node</dt>
+
+
+<dl><dt id="arg-upstream-node">upstream_node<a class="anchor" aria-label="anchor" href="#arg-upstream-node"></a></dt>
 <dd><p>The node from which the network analysis starts.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>The complete network data.</p></dd>
 
 
-<dt>moon_scores</dt>
+<dt id="arg-moon-scores">moon_scores<a class="anchor" aria-label="anchor" href="#arg-moon-scores"></a></dt>
 <dd><p>Scores associated with each node in the network.</p></dd>
 
 
-<dt>keep_upstream_node_peers</dt>
+<dt id="arg-keep-upstream-node-peers">keep_upstream_node_peers<a class="anchor" aria-label="anchor" href="#arg-keep-upstream-node-peers"></a></dt>
 <dd><p>Logical; whether to keep peers of the upstream node. Default is FALSE.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list with two elements: 
+    <p>A list with two elements:
   - `SIF`: A data frame representing the filtered meta network.
   - `ATT`: A data frame representing the updated moon scores.</p>
     </div>
@@ -129,7 +102,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -138,14 +111,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/gmt_to_dataframe.html b/reference/gmt_to_dataframe.html
index f440e8f..e96aa7f 100644
--- a/reference/gmt_to_dataframe.html
+++ b/reference/gmt_to_dataframe.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function is designed to convert a gmt file (gene set file from MSigDB)
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert gmt file to data frame — gmt_to_dataframe • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Convert gmt file to data frame — gmt_to_dataframe"><meta name="description" content="This function is designed to convert a gmt file (gene set file from MSigDB)
 into a two column data frame where the first column corresponds to omic
 features (genes) and the second column to associated terms (pathway the gene
-belongs to). One gene can belong to several pathways."><title>Convert gmt file to data frame — gmt_to_dataframe • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Convert gmt file to data frame — gmt_to_dataframe"><meta property="og:description" content="This function is designed to convert a gmt file (gene set file from MSigDB)
+belongs to). One gene can belong to several pathways."><meta property="og:description" content="This function is designed to convert a gmt file (gene set file from MSigDB)
 into a two column data frame where the first column corresponds to omic
 features (genes) and the second column to associated terms (pathway the gene
-belongs to). One gene can belong to several pathways."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+belongs to). One gene can belong to several pathways."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,64 +13,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Convert gmt file to data frame</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_ORA.R" class="external-link"><code>R/support_ORA.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_ORA.R" class="external-link"><code>R/support_ORA.R</code></a></small>
       <div class="d-none name"><code>gmt_to_dataframe.Rd</code></div>
     </div>
 
@@ -91,19 +64,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>gmtfile</dt>
+
+
+<dl><dt id="arg-gmtfile">gmtfile<a class="anchor" aria-label="anchor" href="#arg-gmtfile"></a></dt>
 <dd><p>a full path name of the gmt file to be converted</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>a two column data frame where the first column corresponds to omic
+    <p>a two column data frame where the first column corresponds to omic
 features and the second column to associated terms (pathways).</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +85,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/index.html b/reference/index.html
index 94a862b..d72d55a 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Function reference"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Package index"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,244 +7,254 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-index">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.png" class="logo" alt=""><h1>Function reference</h1>
+      <img src="../logo.png" class="logo" alt=""><h1>Package index</h1>
     </div>
 
     <div class="section level2">
       <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="#all-functions"></a></h2>
-      
-      
 
-      
-    </div><div id="" class="section level2">
-      
-      
-      
+
+
+
+    </div><div class="section level2">
+
+
+
 
       <dl><dt>
-          
-          <code><a href="HMDB_mapper_vec.html">HMDB_mapper_vec</a></code> 
+
+          <code><a href="HMDB_mapper_vec.html">HMDB_mapper_vec</a></code>
+
         </dt>
         <dd>Toy Input Transcription Data Set</dd>
       </dl><dl><dt>
-          
-          <code><a href="compress_same_children.html">compress_same_children()</a></code> 
+
+          <code><a href="compress_same_children.html">compress_same_children()</a></code>
+
         </dt>
         <dd>Compress Network by Merging Nodes with Identical Children</dd>
       </dl><dl><dt>
-          
-          <code><a href="cosmos_data.html">cosmos_data()</a></code> 
+
+          <code><a href="cosmos_data.html">cosmos_data()</a></code>
+
         </dt>
         <dd>Create Cosmos Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="createLinearColors.html">createLinearColors()</a></code> 
+
+          <code><a href="createLinearColors.html">createLinearColors()</a></code>
+
         </dt>
         <dd>Create Linear Colors Based on Numeric Input</dd>
       </dl><dl><dt>
-          
-          <code><a href="decompress_moon_result.html">decompress_moon_result()</a></code> 
+
+          <code><a href="decompress_moon_result.html">decompress_moon_result()</a></code>
+
         </dt>
         <dd>Decompress Moon Result</dd>
       </dl><dl><dt>
-          
-          <code><a href="decompress_solution_network.html">decompress_solution_network()</a></code> 
+
+          <code><a href="decompress_solution_network.html">decompress_solution_network()</a></code>
+
         </dt>
         <dd>Decompress Solution Network</dd>
       </dl><dl><dt>
-          
-          <code><a href="decoupleRnival.html">decoupleRnival()</a></code> 
+
+          <code><a href="decoupleRnival.html">decoupleRnival()</a></code>
+
         </dt>
         <dd>DecoupleRnival</dd>
       </dl><dl><dt>
-          
-          <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options()</a></code> 
+
+          <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options()</a></code>
+
         </dt>
         <dd>Setting Default CARNIVAL Options</dd>
       </dl><dl><dt>
-          
-          <code><a href="display_node_neighboorhood.html">display_node_neighboorhood()</a></code> 
+
+          <code><a href="display_node_neighboorhood.html">display_node_neighboorhood()</a></code>
+
         </dt>
         <dd>display_node_neighboorhood</dd>
       </dl><dl><dt>
-          
-          <code><a href="extract_nodes_for_ORA.html">extract_nodes_for_ORA()</a></code> 
+
+          <code><a href="extract_nodes_for_ORA.html">extract_nodes_for_ORA()</a></code>
+
         </dt>
         <dd>Extract COSMOS nodes for ORA analysis</dd>
       </dl><dl><dt>
-          
-          <code><a href="filter_incohrent_TF_target.html">filter_incohrent_TF_target()</a></code> 
+
+          <code><a href="filter_incohrent_TF_target.html">filter_incohrent_TF_target()</a></code>
+
         </dt>
         <dd>filter_incohrent_TF_target</dd>
       </dl><dl><dt>
-          
-          <code><a href="format_COSMOS_res.html">format_COSMOS_res()</a></code> 
+
+          <code><a href="format_COSMOS_res.html">format_COSMOS_res()</a></code>
+
         </dt>
         <dd>format_COSMOS_res</dd>
       </dl><dl><dt>
-          
-          <code><a href="format_LR_ressource.html">format_LR_ressource()</a></code> 
+
+          <code><a href="format_LR_ressource.html">format_LR_ressource()</a></code>
+
         </dt>
         <dd>Format Ligand-Receptor Resource</dd>
       </dl><dl><dt>
-          
-          <code><a href="get_moon_scoring_network.html">get_moon_scoring_network()</a></code> 
+
+          <code><a href="get_moon_scoring_network.html">get_moon_scoring_network()</a></code>
+
         </dt>
         <dd>Get Moon Scoring Network</dd>
       </dl><dl><dt>
-          
-          <code><a href="gmt_to_dataframe.html">gmt_to_dataframe()</a></code> 
+
+          <code><a href="gmt_to_dataframe.html">gmt_to_dataframe()</a></code>
+
         </dt>
         <dd>Convert gmt file to data frame</dd>
       </dl><dl><dt>
-          
-          <code><a href="load_tf_regulon_dorothea.html">load_tf_regulon_dorothea()</a></code> 
+
+          <code><a href="load_tf_regulon_dorothea.html">load_tf_regulon_dorothea()</a></code>
+
         </dt>
         <dd>load transcription factor regulon</dd>
       </dl><dl><dt>
-          
-          <code><a href="make_heatmap_color_palette.html">make_heatmap_color_palette()</a></code> 
+
+          <code><a href="make_heatmap_color_palette.html">make_heatmap_color_palette()</a></code>
+
         </dt>
         <dd>Create Heatmap Color Palette</dd>
       </dl><dl><dt>
-          
-          <code><a href="meta_network.html">meta_network</a></code> 
+
+          <code><a href="meta_network.html">meta_network</a></code>
+
         </dt>
         <dd>Meta Prior Knowledge Network</dd>
       </dl><dl><dt>
-          
-          <code><a href="meta_network_cleanup.html">meta_network_cleanup()</a></code> 
+
+          <code><a href="meta_network_cleanup.html">meta_network_cleanup()</a></code>
+
         </dt>
         <dd>meta_network_cleanup</dd>
       </dl><dl><dt>
-          
-          <code><a href="moon.html">moon()</a></code> 
+
+          <code><a href="moon.html">moon()</a></code>
+
         </dt>
         <dd>moon</dd>
       </dl><dl><dt>
-          
-          <code><a href="prepare_metab_inputs.html">prepare_metab_inputs()</a></code> 
+
+          <code><a href="prepare_metab_inputs.html">prepare_metab_inputs()</a></code>
+
         </dt>
         <dd>add metabolic compartment and metab__ prefix to metabolite IDs</dd>
       </dl><dl><dt>
-          
-          <code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling()</a></code> 
+
+          <code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling()</a></code>
+
         </dt>
         <dd>Preprocess COSMOS Inputs For Metabolism to Signaling</dd>
       </dl><dl><dt>
-          
-          <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism()</a></code> 
+
+          <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism()</a></code>
+
         </dt>
         <dd>Preprocess COSMOS Inputs For Signaling to Metabolism</dd>
       </dl><dl><dt>
-          
-          <code><a href="print.cosmos_data.html">print(<i>&lt;cosmos_data&gt;</i>)</a></code> 
+
+          <code><a href="print.cosmos_data.html">print(<i>&lt;cosmos_data&gt;</i>)</a></code>
+
         </dt>
         <dd>Print Cosmos Data Summary Print a summary of cosmos data.</dd>
       </dl><dl><dt>
-          
-          <code><a href="reduce_solution_network.html">reduce_solution_network()</a></code> 
+
+          <code><a href="reduce_solution_network.html">reduce_solution_network()</a></code>
+
         </dt>
         <dd>reduce_solution_network</dd>
       </dl><dl><dt>
-          
-          <code><a href="run_COSMOS_metabolism_to_signaling.html">run_COSMOS_metabolism_to_signaling()</a></code> 
+
+          <code><a href="run_COSMOS_metabolism_to_signaling.html">run_COSMOS_metabolism_to_signaling()</a></code>
+
         </dt>
         <dd>run COSMOS metabolism to signaling</dd>
       </dl><dl><dt>
-          
-          <code><a href="run_COSMOS_signaling_to_metabolism.html">run_COSMOS_signaling_to_metabolism()</a></code> 
+
+          <code><a href="run_COSMOS_signaling_to_metabolism.html">run_COSMOS_signaling_to_metabolism()</a></code>
+
         </dt>
         <dd>run COSMOS signaling to metabolism</dd>
       </dl><dl><dt>
-          
-          <code><a href="toy_RNA.html">toy_RNA</a></code> 
+
+          <code><a href="toy_RNA.html">toy_RNA</a></code>
+
         </dt>
         <dd>Toy Input Transcription Data Set</dd>
       </dl><dl><dt>
-          
-          <code><a href="toy_metabolic_input.html">toy_metabolic_input</a></code> 
+
+          <code><a href="toy_metabolic_input.html">toy_metabolic_input</a></code>
+
         </dt>
         <dd>Toy Metabolic Input Data</dd>
       </dl><dl><dt>
-          
-          <code><a href="toy_network.html">toy_network</a></code> 
+
+          <code><a href="toy_network.html">toy_network</a></code>
+
         </dt>
         <dd>Toy Input Network</dd>
       </dl><dl><dt>
-          
-          <code><a href="toy_signaling_input.html">toy_signaling_input</a></code> 
+
+          <code><a href="toy_signaling_input.html">toy_signaling_input</a></code>
+
         </dt>
         <dd>Toy Signaling Input</dd>
       </dl><dl><dt>
-          
-          <code><a href="translate_column_HMDB.html">translate_column_HMDB()</a></code> 
+
+          <code><a href="translate_column_HMDB.html">translate_column_HMDB()</a></code>
+
         </dt>
         <dd>Translate Column Using HMDB Mapper</dd>
       </dl><dl><dt>
-          
-          <code><a href="translate_res.html">translate_res()</a></code> 
+
+          <code><a href="translate_res.html">translate_res()</a></code>
+
         </dt>
         <dd>translate_res</dd>
       </dl><dl><dt>
-          
-          <code><a href="wide_ulm_res.html">wide_ulm_res()</a></code> 
+
+          <code><a href="wide_ulm_res.html">wide_ulm_res()</a></code>
+
         </dt>
         <dd>Convert ULM Results to Wide Format</dd>
       </dl></div>
@@ -259,14 +266,14 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/load_tf_regulon_dorothea.html b/reference/load_tf_regulon_dorothea.html
index 9588e92..d01f328 100644
--- a/reference/load_tf_regulon_dorothea.html
+++ b/reference/load_tf_regulon_dorothea.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="load the transcription factors from DOROTHEA package and converts 
-gene symbols to EntrezID using org.Hs.eg.db"><title>load transcription factor regulon — load_tf_regulon_dorothea • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="load transcription factor regulon — load_tf_regulon_dorothea"><meta property="og:description" content="load the transcription factors from DOROTHEA package and converts 
-gene symbols to EntrezID using org.Hs.eg.db"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>load transcription factor regulon — load_tf_regulon_dorothea • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="load transcription factor regulon — load_tf_regulon_dorothea"><meta name="description" content="load the transcription factors from DOROTHEA package and converts
+gene symbols to EntrezID using org.Hs.eg.db"><meta property="og:description" content="load the transcription factors from DOROTHEA package and converts
+gene symbols to EntrezID using org.Hs.eg.db"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,69 +9,45 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
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-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>load transcription factor regulon</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/load_tf_regulon_dorothea.R" class="external-link"><code>R/load_tf_regulon_dorothea.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/load_tf_regulon_dorothea.R" class="external-link"><code>R/load_tf_regulon_dorothea.R</code></a></small>
       <div class="d-none name"><code>load_tf_regulon_dorothea.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>load the transcription factors from <code>DOROTHEA</code> package and converts 
+    <p>load the transcription factors from <code>DOROTHEA</code> package and converts
 gene symbols to EntrezID using org.Hs.eg.db</p>
     </div>
 
@@ -85,20 +58,18 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>confidence</dt>
+
+
+<dl><dt id="arg-confidence">confidence<a class="anchor" aria-label="anchor" href="#arg-confidence"></a></dt>
 <dd><p>strong vector (by default: c("A","B","C")). Subset of {A, B,
- C, D, E}. See the `dorothea` for the meaning of confidence levels. 
+ C, D, E}. See the `dorothea` for the meaning of confidence levels.
 package for further details.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>returns a PKN of a form of a data table. Each row is an interaction.
+    <p>returns a PKN of a form of a data table. Each row is an interaction.
 Columns names are:</p>
-
-
 <p>- `tf` transcription factor
 - `confidence` class of confidence
 - `target` target gene
@@ -124,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 13,213 more rows</span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -133,14 +104,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/make_heatmap_color_palette.html b/reference/make_heatmap_color_palette.html
index d15e610..b6c7d63 100644
--- a/reference/make_heatmap_color_palette.html
+++ b/reference/make_heatmap_color_palette.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function generates a color palette suitable for heatmaps based on the values in a matrix. It uses the `createLinearColors` function to generate separate color gradients for positive and negative values."><title>Create Heatmap Color Palette — make_heatmap_color_palette • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Heatmap Color Palette — make_heatmap_color_palette"><meta property="og:description" content="This function generates a color palette suitable for heatmaps based on the values in a matrix. It uses the `createLinearColors` function to generate separate color gradients for positive and negative values."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create Heatmap Color Palette — make_heatmap_color_palette • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create Heatmap Color Palette — make_heatmap_color_palette"><meta name="description" content="This function generates a color palette suitable for heatmaps based on the values in a matrix. It uses the `createLinearColors` function to generate separate color gradients for positive and negative values."><meta property="og:description" content="This function generates a color palette suitable for heatmaps based on the values in a matrix. It uses the `createLinearColors` function to generate separate color gradients for positive and negative values."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Create Heatmap Color Palette</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_pheatmap.R" class="external-link"><code>R/support_pheatmap.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_pheatmap.R" class="external-link"><code>R/support_pheatmap.R</code></a></small>
       <div class="d-none name"><code>make_heatmap_color_palette.Rd</code></div>
     </div>
 
@@ -82,15 +55,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>my_matrix</dt>
+
+
+<dl><dt id="arg-my-matrix">my_matrix<a class="anchor" aria-label="anchor" href="#arg-my-matrix"></a></dt>
 <dd><p>A numeric matrix for which the heatmap color palette is to be generated.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A character vector of colors representing the heatmap color palette based on the input matrix values.</p>
+    <p>A character vector of colors representing the heatmap color palette based on the input matrix values.</p>
     </div>
 
     <div class="section level2">
@@ -103,7 +76,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/meta_network.html b/reference/meta_network.html
index 4117180..c60e761 100644
--- a/reference/meta_network.html
+++ b/reference/meta_network.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Comprehensive Prior Knowledge Network (PKN), which combines signaling and
-metabolic interaction networks.  The network was constructed using the Recon3D 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Meta Prior Knowledge Network — meta_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Meta Prior Knowledge Network — meta_network"><meta name="description" content="Comprehensive Prior Knowledge Network (PKN), which combines signaling and
+metabolic interaction networks.  The network was constructed using the Recon3D
 and STITCH metabolic networks as well as the signaling network from
-OmniPath."><title>Meta Prior Knowledge Network — meta_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Meta Prior Knowledge Network — meta_network"><meta property="og:description" content="Comprehensive Prior Knowledge Network (PKN), which combines signaling and
-metabolic interaction networks.  The network was constructed using the Recon3D 
+OmniPath."><meta property="og:description" content="Comprehensive Prior Knowledge Network (PKN), which combines signaling and
+metabolic interaction networks.  The network was constructed using the Recon3D
 and STITCH metabolic networks as well as the signaling network from
-OmniPath."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+OmniPath."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,70 +13,46 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
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-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Meta Prior Knowledge Network</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/meta_network.R" class="external-link"><code>R/meta_network.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/meta_network.R" class="external-link"><code>R/meta_network.R</code></a></small>
       <div class="d-none name"><code>meta_network.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Comprehensive Prior Knowledge Network (PKN), which combines signaling and
-metabolic interaction networks.  The network was constructed using the Recon3D 
+metabolic interaction networks.  The network was constructed using the Recon3D
 and STITCH metabolic networks as well as the signaling network from
 OmniPath.</p>
     </div>
@@ -101,20 +74,20 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
     <dt><code>target</code></dt>
 <dd><p>Target node, either metabolite or protein</p></dd>
 
-  A detailed description of the identifier formatting can be found under 
+  A detailed description of the identifier formatting can be found under
   https://metapkn.omnipathdb.org/00__README.txt.
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>The network is available in Omnipath:
-  <a href="https://metapkn.omnipathdb.org/metapkn__20200122.txt" class="external-link">https://metapkn.omnipathdb.org/metapkn__20200122.txt</a>, the scripts 
+  <a href="https://metapkn.omnipathdb.org/metapkn__20200122.txt" class="external-link">https://metapkn.omnipathdb.org/metapkn__20200122.txt</a>, the scripts
   used for the build of the network are available under
   <a href="https://github.com/saezlab/Meta_PKN" class="external-link">https://github.com/saezlab/Meta_PKN</a>.</p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular 
+    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular
   Systems Biology</em>. <b>17</b>, e9730.</p>
     </div>
 
@@ -124,7 +97,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -133,14 +106,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/meta_network_cleanup.html b/reference/meta_network_cleanup.html
index de281bd..d8c2cf4 100644
--- a/reference/meta_network_cleanup.html
+++ b/reference/meta_network_cleanup.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function cleans up a meta network data frame by removing self-interactions,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>meta_network_cleanup — meta_network_cleanup • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="meta_network_cleanup — meta_network_cleanup"><meta name="description" content="This function cleans up a meta network data frame by removing self-interactions,
 calculating the mean interaction values for duplicated source-target pairs, and
-keeping only interactions with values of 1 or -1."><title>meta_network_cleanup — meta_network_cleanup • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="meta_network_cleanup — meta_network_cleanup"><meta property="og:description" content="This function cleans up a meta network data frame by removing self-interactions,
+keeping only interactions with values of 1 or -1."><meta property="og:description" content="This function cleans up a meta network data frame by removing self-interactions,
 calculating the mean interaction values for duplicated source-target pairs, and
-keeping only interactions with values of 1 or -1."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+keeping only interactions with values of 1 or -1."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,64 +11,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
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-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>meta_network_cleanup</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>meta_network_cleanup.Rd</code></div>
     </div>
 
@@ -88,15 +61,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>meta_network</dt>
+
+
+<dl><dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A data frame with columns 'source', 'interaction', and 'target'.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A cleaned up meta network data frame.</p>
+    <p>A cleaned up meta network data frame.</p>
     </div>
 
     <div class="section level2">
@@ -137,7 +110,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -146,14 +119,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/moon.html b/reference/moon.html
index 04f47a6..3da2822 100644
--- a/reference/moon.html
+++ b/reference/moon.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Iteratively propagate downstream input activity through a signed directed network
-using the weighted mean enrichment score from decoupleR package"><title>moon — moon • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="moon — moon"><meta property="og:description" content="Iteratively propagate downstream input activity through a signed directed network
-using the weighted mean enrichment score from decoupleR package"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>moon — moon • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="moon — moon"><meta name="description" content="Iteratively propagate downstream input activity through a signed directed network
+using the weighted mean enrichment score from decoupleR package"><meta property="og:description" content="Iteratively propagate downstream input activity through a signed directed network
+using the weighted mean enrichment score from decoupleR package"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>moon</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>moon.Rd</code></div>
     </div>
 
@@ -94,43 +67,43 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>upstream_input</dt>
+
+
+<dl><dt id="arg-upstream-input">upstream_input<a class="anchor" aria-label="anchor" href="#arg-upstream-input"></a></dt>
 <dd><p>A named vector with up_stream nodes and their corresponding activity.</p></dd>
 
 
-<dt>downstream_input</dt>
+<dt id="arg-downstream-input">downstream_input<a class="anchor" aria-label="anchor" href="#arg-downstream-input"></a></dt>
 <dd><p>A named vector with down_stream nodes and their corresponding activity.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A network data frame containing signed directed prior knowledge of molecular interactions.</p></dd>
 
 
-<dt>n_layers</dt>
+<dt id="arg-n-layers">n_layers<a class="anchor" aria-label="anchor" href="#arg-n-layers"></a></dt>
 <dd><p>The number of layers that will be propagated upstream.</p></dd>
 
 
-<dt>n_perm</dt>
+<dt id="arg-n-perm">n_perm<a class="anchor" aria-label="anchor" href="#arg-n-perm"></a></dt>
 <dd><p>The number of permutations to use in decoupleR's algorithm.</p></dd>
 
 
-<dt>downstream_cutoff</dt>
+<dt id="arg-downstream-cutoff">downstream_cutoff<a class="anchor" aria-label="anchor" href="#arg-downstream-cutoff"></a></dt>
 <dd><p>If downstream measurments should be included above a given threshold</p></dd>
 
 
-<dt>statistic</dt>
+<dt id="arg-statistic">statistic<a class="anchor" aria-label="anchor" href="#arg-statistic"></a></dt>
 <dd><p>the decoupleR stat to consider: "wmean", "norm_wmean", or "ulm"</p></dd>
 
 
-<dt>return_levels</dt>
+<dt id="arg-return-levels">return_levels<a class="anchor" aria-label="anchor" href="#arg-return-levels"></a></dt>
 <dd><p>true or false, if true the layers that the protein belongs to will be returned alongside the scores</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame containing the score of the nodes upstream of the 
+    <p>A data frame containing the score of the nodes upstream of the
 downstream input based on the iterative propagation</p>
     </div>
 
@@ -157,7 +130,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> E      E  -1.5     0</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -166,14 +139,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
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-  
+
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diff --git a/reference/prepare_metab_inputs.html b/reference/prepare_metab_inputs.html
index 82022f7..074f26b 100644
--- a/reference/prepare_metab_inputs.html
+++ b/reference/prepare_metab_inputs.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function adds metabolic compartments to the metabolic identifiers provided by the user."><title>add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs"><meta property="og:description" content="This function adds metabolic compartments to the metabolic identifiers provided by the user."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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       <img src="../logo.png" class="logo" alt=""><h1>add metabolic compartment and metab__ prefix to metabolite IDs</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/prepare_metab_inputs.R" class="external-link"><code>R/prepare_metab_inputs.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/prepare_metab_inputs.R" class="external-link"><code>R/prepare_metab_inputs.R</code></a></small>
       <div class="d-none name"><code>prepare_metab_inputs.Rd</code></div>
     </div>
 
@@ -82,22 +55,22 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>metab_input</dt>
+
+
+<dl><dt id="arg-metab-input">metab_input<a class="anchor" aria-label="anchor" href="#arg-metab-input"></a></dt>
 <dd><p>a named  vector with matebolic statistics as inputs and metabolite identifiers as names</p></dd>
 
 
-<dt>compartment_codes</dt>
+<dt id="arg-compartment-codes">compartment_codes<a class="anchor" aria-label="anchor" href="#arg-compartment-codes"></a></dt>
 <dd><p>a character vector, the desired compartment codes to be added. Possible values are "r", "c", "e", "x", "m", "l", "n" and "g"</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>a named vector with the compartment code and prefixed added to the names</p>
+    <p>a named vector with the compartment code and prefixed added to the names</p>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -106,14 +79,14 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/preprocess_COSMOS_metabolism_to_signaling.html b/reference/preprocess_COSMOS_metabolism_to_signaling.html
index 8090e98..5b8d9e2 100644
--- a/reference/preprocess_COSMOS_metabolism_to_signaling.html
+++ b/reference/preprocess_COSMOS_metabolism_to_signaling.html
@@ -1,20 +1,17 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling"><meta name="description" content="Runs checks on the input data and simplifies the prior knowledge network.
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
-CARNIVAL and the interactions between TF and genes are filtered again."><title>Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling"><meta property="og:description" content="Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:description" content="Runs checks on the input data and simplifies the prior knowledge network.
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
-CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -22,73 +19,49 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
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-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
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-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Preprocess COSMOS Inputs For Metabolism to Signaling</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/preprocess_COSMOS_metabolism_to_signaling.R" class="external-link"><code>R/preprocess_COSMOS_metabolism_to_signaling.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/preprocess_COSMOS_metabolism_to_signaling.R" class="external-link"><code>R/preprocess_COSMOS_metabolism_to_signaling.R</code></a></small>
       <div class="d-none name"><code>preprocess_COSMOS_metabolism_to_signaling.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
 CARNIVAL and the interactions between TF and genes are filtered again.</p>
     </div>
@@ -112,81 +85,79 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>meta_network</dt>
+
+
+<dl><dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>prior knowledge network (PKN). A PKN released with COSMOS
-and derived from Omnipath, STITCHdb and Recon3D can be used. See details on 
+and derived from Omnipath, STITCHdb and Recon3D can be used. See details on
 the data <code><a href="meta_network.html">meta_network</a></code>.</p></dd>
 
 
-<dt>tf_regulon</dt>
+<dt id="arg-tf-regulon">tf_regulon<a class="anchor" aria-label="anchor" href="#arg-tf-regulon"></a></dt>
 <dd><p>collection of transcription factor - target interactions.
-A default collection from dorothea can be obtained by the 
+A default collection from dorothea can be obtained by the
 <code><a href="load_tf_regulon_dorothea.html">load_tf_regulon_dorothea</a></code> function.</p></dd>
 
 
-<dt>signaling_data</dt>
-<dd><p>numerical vector, where names are signaling nodes 
-in the PKN and values are from {1, 0, -1}. Continuous data will be 
+<dt id="arg-signaling-data">signaling_data<a class="anchor" aria-label="anchor" href="#arg-signaling-data"></a></dt>
+<dd><p>numerical vector, where names are signaling nodes
+in the PKN and values are from {1, 0, -1}. Continuous data will be
 discretized using the <code><a href="https://rdrr.io/r/base/sign.html" class="external-link">sign</a></code> function.</p></dd>
 
 
-<dt>metabolic_data</dt>
-<dd><p>numerical vector, where names are metabolic nodes 
-in the PKN and values are continuous values that represents log2 fold change 
-or t-values from a differential analysis. These values are compared to 
+<dt id="arg-metabolic-data">metabolic_data<a class="anchor" aria-label="anchor" href="#arg-metabolic-data"></a></dt>
+<dd><p>numerical vector, where names are metabolic nodes
+in the PKN and values are continuous values that represents log2 fold change
+or t-values from a differential analysis. These values are compared to
 the simulation results (simulated nodes can take value -1, 0 or 1)</p></dd>
 
 
-<dt>diff_expression_data</dt>
-<dd><p>(optional) numerical vector that represents the 
+<dt id="arg-diff-expression-data">diff_expression_data<a class="anchor" aria-label="anchor" href="#arg-diff-expression-data"></a></dt>
+<dd><p>(optional) numerical vector that represents the
 results of a differential gene expression analysis. Names are gene
 names using gene symbole and values are log fold change or
  t-values. We use the “<code>diff_exp_threshold</code>” parameter to decide
- which genes changed significantly.  Genes with NA values are considered none 
+ which genes changed significantly.  Genes with NA values are considered none
  expressed and they will be removed from the TF-gene expression interactions.</p></dd>
 
 
-<dt>diff_exp_threshold</dt>
+<dt id="arg-diff-exp-threshold">diff_exp_threshold<a class="anchor" aria-label="anchor" href="#arg-diff-exp-threshold"></a></dt>
 <dd><p>threshold parameter (default 1) used to binarize
 the values of “<code>diff_expression_data</code>”.</p></dd>
 
 
-<dt>maximum_network_depth</dt>
-<dd><p>integer &gt; 0 (default: 8). Nodes that are further 
+<dt id="arg-maximum-network-depth">maximum_network_depth<a class="anchor" aria-label="anchor" href="#arg-maximum-network-depth"></a></dt>
+<dd><p>integer &gt; 0 (default: 8). Nodes that are further
 than “<code>maximum_network_depth</code>” steps from the signaling nodes on
 the directed graph of the PKN are considered non-reachable and are removed.</p></dd>
 
 
-<dt>expressed_genes</dt>
-<dd><p>character vector. Names of nodes that are expressed. By 
+<dt id="arg-expressed-genes">expressed_genes<a class="anchor" aria-label="anchor" href="#arg-expressed-genes"></a></dt>
+<dd><p>character vector. Names of nodes that are expressed. By
 default we consider all the nodes that appear in <code>diff_expression_data</code> with
 a numeric value (i.e. nodes with NA are removed)</p></dd>
 
 
-<dt>remove_unexpressed_nodes</dt>
-<dd><p>if TRUE (default) removes nodes from the PKN 
+<dt id="arg-remove-unexpressed-nodes">remove_unexpressed_nodes<a class="anchor" aria-label="anchor" href="#arg-remove-unexpressed-nodes"></a></dt>
+<dd><p>if TRUE (default) removes nodes from the PKN
 that are not expressed, see input “<code>expressed_genes</code>”.</p></dd>
 
 
-<dt>filter_tf_gene_interaction_by_optimization</dt>
-<dd><p>(default:TRUE), if TRUE then runs 
+<dt id="arg-filter-tf-gene-interaction-by-optimization">filter_tf_gene_interaction_by_optimization<a class="anchor" aria-label="anchor" href="#arg-filter-tf-gene-interaction-by-optimization"></a></dt>
+<dd><p>(default:TRUE), if TRUE then runs
 a network optimization that estimates TF activity not included in the inputs
-and checks the consistency between the estimated activity and change in gene 
+and checks the consistency between the estimated activity and change in gene
 expression. Removes interactions where TF and gene expression are inconsistent</p></dd>
 
 
-<dt>CARNIVAL_options</dt>
-<dd><p>list that controls the options of CARNIVAL. See details 
+<dt id="arg-carnival-options">CARNIVAL_options<a class="anchor" aria-label="anchor" href="#arg-carnival-options"></a></dt>
+<dd><p>list that controls the options of CARNIVAL. See details
 in <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>cosmos_data object with the following fields:</p>
-<p></p>
-<dl><dt><code>meta_network</code></dt>
+    <p>cosmos_data object with the following fields:</p><dl><dt><code>meta_network</code></dt>
 <dd><p>Filtered PKN</p></dd>
 
     <dt><code>tf_regulon</code></dt>
@@ -194,18 +165,18 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <dt><code>signaling_data_bin</code></dt>
 <dd><p>Binarised signaling data</p></dd>
- 
+
     <dt><code>metabolic_data</code></dt>
 <dd><p>Metabolomics data</p></dd>
 
     <dt><code>diff_expression_data_bin</code></dt>
 <dd><p>Binarized gene expression data</p></dd>
- 
+
     <dt><code>optimized_network</code></dt>
-<dd><p>Initial optimized network if 
+<dd><p>Initial optimized network if
     <code>filter_tf_gene_interaction_by_optimization is TRUE</code></p></dd>
 
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -244,16 +215,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_39d24_06_2024n47.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_36d15_07_2024n47.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_39d24_06_2024n47.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_36d15_07_2024n47.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">842</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -263,14 +234,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:36 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -280,7 +251,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -289,14 +260,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/reference/preprocess_COSMOS_signaling_to_metabolism.html b/reference/preprocess_COSMOS_signaling_to_metabolism.html
index e0fe0d2..842a827 100644
--- a/reference/preprocess_COSMOS_signaling_to_metabolism.html
+++ b/reference/preprocess_COSMOS_signaling_to_metabolism.html
@@ -1,20 +1,17 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism"><meta name="description" content="Runs checks on the input data and simplifies the prior knowledge network.
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
-CARNIVAL and the interactions between TF and genes are filtered again."><title>Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism"><meta property="og:description" content="Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:description" content="Runs checks on the input data and simplifies the prior knowledge network.
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
-CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+CARNIVAL and the interactions between TF and genes are filtered again."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -22,73 +19,49 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
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+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Preprocess COSMOS Inputs For Signaling to Metabolism</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/preprocess_COSMOS_signaling_to_metabolism.R" class="external-link"><code>R/preprocess_COSMOS_signaling_to_metabolism.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/preprocess_COSMOS_signaling_to_metabolism.R" class="external-link"><code>R/preprocess_COSMOS_signaling_to_metabolism.R</code></a></small>
       <div class="d-none name"><code>preprocess_COSMOS_signaling_to_metabolism.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Runs checks on the input data and simplifies the prior knowledge network.
-Simplification includes the removal of (1) nodes that are not reachable from 
+Simplification includes the removal of (1) nodes that are not reachable from
 signaling nodes and  (2) interactions between transcription factors and target
 genes if the target gene does not respond or the response is contradictory
-with the change in the transcription factor activity. 
+with the change in the transcription factor activity.
 Optionally, further TF activities are estimated via network optimization via
 CARNIVAL and the interactions between TF and genes are filtered again.</p>
     </div>
@@ -112,33 +85,35 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>meta_network</dt>
+
+
+<dl><dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>prior knowledge network (PKN). A PKN released with COSMOS
-and derived from Omnipath, STITCHdb and Recon3D can be used. See details on 
+and derived from Omnipath, STITCHdb and Recon3D can be used. See details on
 the data <code><a href="meta_network.html">meta_network</a></code>.</p></dd>
 
 
-<dt>tf_regulon</dt>
+<dt id="arg-tf-regulon">tf_regulon<a class="anchor" aria-label="anchor" href="#arg-tf-regulon"></a></dt>
 <dd><p>collection of transcription factor - target interactions.
-A default collection from dorothea can be obtained by the 
+A default collection from dorothea can be obtained by the
 <code><a href="load_tf_regulon_dorothea.html">load_tf_regulon_dorothea</a></code> function.</p></dd>
 
 
-<dt>signaling_data</dt>
-<dd><p>numerical vector, where names are signaling nodes 
-in the PKN and values are from {1, 0, -1}. Continuous data will be 
+<dt id="arg-signaling-data">signaling_data<a class="anchor" aria-label="anchor" href="#arg-signaling-data"></a></dt>
+<dd><p>numerical vector, where names are signaling nodes
+in the PKN and values are from {1, 0, -1}. Continuous data will be
 discretized using the <code><a href="https://rdrr.io/r/base/sign.html" class="external-link">sign</a></code> function.</p></dd>
 
 
-<dt>metabolic_data</dt>
-<dd><p>numerical vector, where names are metabolic nodes 
-in the PKN and values are continuous values that represents log2 fold change 
-or t-values from a differential analysis. These values are compared to 
+<dt id="arg-metabolic-data">metabolic_data<a class="anchor" aria-label="anchor" href="#arg-metabolic-data"></a></dt>
+<dd><p>numerical vector, where names are metabolic nodes
+in the PKN and values are continuous values that represents log2 fold change
+or t-values from a differential analysis. These values are compared to
 the simulation results (simulated nodes can take value -1, 0 or 1)</p></dd>
 
 
-<dt>diff_expression_data</dt>
-<dd><p>(optional) numerical vector that represents the 
+<dt id="arg-diff-expression-data">diff_expression_data<a class="anchor" aria-label="anchor" href="#arg-diff-expression-data"></a></dt>
+<dd><p>(optional) numerical vector that represents the
 results of a differential gene expression analysis. Names are gene
 names using gene symbole and values are log fold change or
  t-values.  We use the “<code>diff_exp_threshold</code>” parameter to decide
@@ -146,47 +121,43 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
  expressed and they will be removed from the TF-gene expression interactions.</p></dd>
 
 
-<dt>diff_exp_threshold</dt>
+<dt id="arg-diff-exp-threshold">diff_exp_threshold<a class="anchor" aria-label="anchor" href="#arg-diff-exp-threshold"></a></dt>
 <dd><p>threshold parameter (default 1) used to binarize
 the values of “<code>diff_expression_data</code>”.</p></dd>
 
 
-<dt>maximum_network_depth</dt>
-<dd><p>integer &gt; 0 (default: 8). Nodes that are further 
-than “<code>maximum_network_depth</code>” steps from the signaling nodes on 
+<dt id="arg-maximum-network-depth">maximum_network_depth<a class="anchor" aria-label="anchor" href="#arg-maximum-network-depth"></a></dt>
+<dd><p>integer &gt; 0 (default: 8). Nodes that are further
+than “<code>maximum_network_depth</code>” steps from the signaling nodes on
 the directed graph of the PKN are considered non-reachable and are removed.</p></dd>
 
 
-<dt>expressed_genes</dt>
-<dd><p>character vector. Names of nodes that are expressed. By 
+<dt id="arg-expressed-genes">expressed_genes<a class="anchor" aria-label="anchor" href="#arg-expressed-genes"></a></dt>
+<dd><p>character vector. Names of nodes that are expressed. By
 default we consider all the nodes that appear in <code>diff_expression_data</code> with
 a numeric value (i.e. nodes with NA are removed)</p></dd>
 
 
-<dt>remove_unexpressed_nodes</dt>
-<dd><p>if TRUE (default) removes nodes from the PKN 
+<dt id="arg-remove-unexpressed-nodes">remove_unexpressed_nodes<a class="anchor" aria-label="anchor" href="#arg-remove-unexpressed-nodes"></a></dt>
+<dd><p>if TRUE (default) removes nodes from the PKN
 that are not expressed, see input “<code>expressed_genes</code>”.</p></dd>
 
 
-<dt>filter_tf_gene_interaction_by_optimization</dt>
-<dd><p>(default:TRUE), if TRUE then runs 
+<dt id="arg-filter-tf-gene-interaction-by-optimization">filter_tf_gene_interaction_by_optimization<a class="anchor" aria-label="anchor" href="#arg-filter-tf-gene-interaction-by-optimization"></a></dt>
+<dd><p>(default:TRUE), if TRUE then runs
 a network optimization that estimates TF activity not included in the inputs
-and checks the consistency between the estimated activity and change in gene 
+and checks the consistency between the estimated activity and change in gene
 expression. Removes interactions where TF and gene expression are inconsistent</p></dd>
 
 
-<dt>CARNIVAL_options</dt>
-<dd><p>list that controls the options of CARNIVAL. See details 
+<dt id="arg-carnival-options">CARNIVAL_options<a class="anchor" aria-label="anchor" href="#arg-carnival-options"></a></dt>
+<dd><p>list that controls the options of CARNIVAL. See details
 in <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>cosmos_data object with the following fields:</p>
-<p></p>
-<dl><dt><code>meta_network</code></dt>
+    <p>cosmos_data object with the following fields:</p><dl><dt><code>meta_network</code></dt>
 <dd><p>Filtered PKN</p></dd>
 
     <dt><code>tf_regulon</code></dt>
@@ -194,18 +165,18 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <dt><code>signaling_data_bin</code></dt>
 <dd><p>Binarised signaling data</p></dd>
- 
+
     <dt><code>metabolic_data</code></dt>
 <dd><p>Metabolomics data</p></dd>
 
     <dt><code>diff_expression_data_bin</code></dt>
 <dd><p>Binarized gene expression data</p></dd>
- 
+
     <dt><code>optimized_network</code></dt>
-<dd><p>Initial optimized network if 
+<dd><p>Initial optimized network if
     <code>filter_tf_gene_interaction_by_optimization is TRUE</code></p></dd>
 
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@@ -242,16 +213,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_39d24_06_2024n31.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_37d15_07_2024n31.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_39d24_06_2024n31.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:39 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_37d15_07_2024n31.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -261,14 +232,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:40 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:37 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -278,7 +249,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS: 2975 of the 5321 transcription factor targets were found in expression data"</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -287,14 +258,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/reference/print.cosmos_data.html b/reference/print.cosmos_data.html
index e5bd9d6..9d1dd5c 100644
--- a/reference/print.cosmos_data.html
+++ b/reference/print.cosmos_data.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Print Cosmos Data Summary Print a summary of cosmos data.</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/cosmos_data.R" class="external-link"><code>R/cosmos_data.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/cosmos_data.R" class="external-link"><code>R/cosmos_data.R</code></a></small>
       <div class="d-none name"><code>print.cosmos_data.Rd</code></div>
     </div>
 
@@ -80,35 +53,35 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for cosmos_data</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'cosmos_data'</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>x</dt>
-<dd><p><code><a href="cosmos_data.html">cosmos_data</a></code> object.  Use the 
-<code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> or 
-<code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> functions to 
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dd><p><code><a href="cosmos_data.html">cosmos_data</a></code> object.  Use the
+<code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> or
+<code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> functions to
 create one.</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>Further print arguments passed to or from other methods.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>input (invisible)</p>
+    <p>input (invisible)</p>
     </div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
     <div class="dont-index"><p><code><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></code>, <code><a href="cosmos_data.html">cosmos_data</a></code></p></div>
     </div>
 
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -117,14 +90,14 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/reduce_solution_network.html b/reference/reduce_solution_network.html
index c784d19..15008ae 100644
--- a/reference/reduce_solution_network.html
+++ b/reference/reduce_solution_network.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Reduces a solution network based on a decoupling analysis of upstream and downstream gene expression,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>reduce_solution_network — reduce_solution_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="reduce_solution_network — reduce_solution_network"><meta name="description" content="Reduces a solution network based on a decoupling analysis of upstream and downstream gene expression,
 by filtering out edges that do not meet a consistency threshold, and limiting the network to a
-certain number of steps from upstream input nodes."><title>reduce_solution_network — reduce_solution_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="reduce_solution_network — reduce_solution_network"><meta property="og:description" content="Reduces a solution network based on a decoupling analysis of upstream and downstream gene expression,
+certain number of steps from upstream input nodes."><meta property="og:description" content="Reduces a solution network based on a decoupling analysis of upstream and downstream gene expression,
 by filtering out edges that do not meet a consistency threshold, and limiting the network to a
-certain number of steps from upstream input nodes."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+certain number of steps from upstream input nodes."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,64 +11,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>reduce_solution_network</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>reduce_solution_network.Rd</code></div>
     </div>
 
@@ -95,35 +68,35 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>decoupleRnival_res</dt>
+
+
+<dl><dt id="arg-decouplernival-res">decoupleRnival_res<a class="anchor" aria-label="anchor" href="#arg-decouplernival-res"></a></dt>
 <dd><p>A data frame resulting from the decoupleRnival function.</p></dd>
 
 
-<dt>meta_network</dt>
+<dt id="arg-meta-network">meta_network<a class="anchor" aria-label="anchor" href="#arg-meta-network"></a></dt>
 <dd><p>A network data frame containing signed directed prior knowledge of molecular interactions.</p></dd>
 
 
-<dt>cutoff</dt>
+<dt id="arg-cutoff">cutoff<a class="anchor" aria-label="anchor" href="#arg-cutoff"></a></dt>
 <dd><p>The consistency threshold for filtering edges from the solution network.</p></dd>
 
 
-<dt>upstream_input</dt>
+<dt id="arg-upstream-input">upstream_input<a class="anchor" aria-label="anchor" href="#arg-upstream-input"></a></dt>
 <dd><p>A named vector with up_stream nodes and their corresponding activity.</p></dd>
 
 
-<dt>RNA_input</dt>
+<dt id="arg-rna-input">RNA_input<a class="anchor" aria-label="anchor" href="#arg-rna-input"></a></dt>
 <dd><p>A named vector containing differential gene expression data.</p></dd>
 
 
-<dt>n_steps</dt>
+<dt id="arg-n-steps">n_steps<a class="anchor" aria-label="anchor" href="#arg-n-steps"></a></dt>
 <dd><p>The maximum number of steps from upstream input nodes to include in the solution network.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A list containing the solution network (SIF) and an attribute table (ATT) with gene expression data.</p>
+    <p>A list containing the solution network (SIF) and an attribute table (ATT) with gene expression data.</p>
     </div>
 
     <div class="section level2">
@@ -161,7 +134,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 3     D  2.00000       0.7</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -170,14 +143,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/run_COSMOS_metabolism_to_signaling.html b/reference/run_COSMOS_metabolism_to_signaling.html
index bffca04..37ce97f 100644
--- a/reference/run_COSMOS_metabolism_to_signaling.html
+++ b/reference/run_COSMOS_metabolism_to_signaling.html
@@ -1,16 +1,13 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Runs COSMOS from metabolism to signaling.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimization that (1) 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling"><meta name="description" content="Runs COSMOS from metabolism to signaling.  This function uses CARNIVAL to find
+a subset of the prior knowledge network based on optimization that (1)
 includes the most measured and input nodes and (2) which is in agreement with
-the data.  Use preprocess_COSMOS_metabolism_to_signaling to 
-prepare the the inputs, measurements and the prior knowledge network."><title>run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling"><meta property="og:description" content="Runs COSMOS from metabolism to signaling.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimization that (1) 
+the data.  Use preprocess_COSMOS_metabolism_to_signaling to
+prepare the the inputs, measurements and the prior knowledge network."><meta property="og:description" content="Runs COSMOS from metabolism to signaling.  This function uses CARNIVAL to find
+a subset of the prior knowledge network based on optimization that (1)
 includes the most measured and input nodes and (2) which is in agreement with
-the data.  Use preprocess_COSMOS_metabolism_to_signaling to 
-prepare the the inputs, measurements and the prior knowledge network."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+the data.  Use preprocess_COSMOS_metabolism_to_signaling to
+prepare the the inputs, measurements and the prior knowledge network."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -18,72 +15,48 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>run COSMOS metabolism to signaling</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/run_COSMOS_metabolism_to_signaling.R" class="external-link"><code>R/run_COSMOS_metabolism_to_signaling.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/run_COSMOS_metabolism_to_signaling.R" class="external-link"><code>R/run_COSMOS_metabolism_to_signaling.R</code></a></small>
       <div class="d-none name"><code>run_COSMOS_metabolism_to_signaling.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Runs COSMOS from metabolism to signaling.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimization that (1) 
+a subset of the prior knowledge network based on optimization that (1)
 includes the most measured and input nodes and (2) which is in agreement with
-the data.  Use <code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> to 
+the data.  Use <code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> to
 prepare the the inputs, measurements and the prior knowledge network.</p>
     </div>
 
@@ -97,30 +70,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>data</dt>
-<dd><p><code><a href="cosmos_data.html">cosmos_data</a></code> object.  Use the 
-<code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> function to create 
+
+
+<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
+<dd><p><code><a href="cosmos_data.html">cosmos_data</a></code> object.  Use the
+<code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code> function to create
 an instance.</p></dd>
 
 
-<dt>CARNIVAL_options</dt>
-<dd><p>List that controls the options of CARNIVAL. See details 
+<dt id="arg-carnival-options">CARNIVAL_options<a class="anchor" aria-label="anchor" href="#arg-carnival-options"></a></dt>
+<dd><p>List that controls the options of CARNIVAL. See details
 in <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List with the following elements:</p>
-<p></p>
-<dl><dt><code>weightedSIF</code></dt>
-<dd><p>The averaged networks found by 
-    optimization in a format of a Simple Interaction network, i.e. each row 
+    <p>List with the following elements:</p><dl><dt><code>weightedSIF</code></dt>
+<dd><p>The averaged networks found by
+    optimization in a format of a Simple Interaction network, i.e. each row
     codes an edge</p></dd>
 
     <dt><code>N_networks</code></dt>
-<dd><p>Number of solutions found by the 
+<dd><p>Number of solutions found by the
     optimization</p></dd>
 
     <dt><code>nodesAttributes</code></dt>
@@ -133,11 +104,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <dd><p>Node activity in each
     network</p></dd>
 
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code>,  
+    <div class="dont-index"><p><code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code>,
   <code><a href="https://rdrr.io/pkg/CARNIVAL/man/runCARNIVAL.html" class="external-link">runCARNIVAL</a></code>, <code><a href="cosmos_data.html">cosmos_data</a></code></p></div>
     </div>
 
@@ -169,16 +140,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n68.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n68.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n68.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n68.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">842</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -188,14 +159,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -210,16 +181,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign().</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n73.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n73.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n73.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n73.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">842</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -229,19 +200,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -250,14 +221,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
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diff --git a/reference/run_COSMOS_signaling_to_metabolism.html b/reference/run_COSMOS_signaling_to_metabolism.html
index 7689c4b..bc9c140 100644
--- a/reference/run_COSMOS_signaling_to_metabolism.html
+++ b/reference/run_COSMOS_signaling_to_metabolism.html
@@ -1,16 +1,13 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Runs COSMOS from signaling to metabolism.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimisation that (1) 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism"><meta name="description" content="Runs COSMOS from signaling to metabolism.  This function uses CARNIVAL to find
+a subset of the prior knowledge network based on optimisation that (1)
 includes the most measured and input nodes and (2) which is in agreement with
 the data.  Use preprocess_COSMOS_signaling_to_metabolism to
-prepare inputs, measurements and prior knowledge network."><title>run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism"><meta property="og:description" content="Runs COSMOS from signaling to metabolism.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimisation that (1) 
+prepare inputs, measurements and prior knowledge network."><meta property="og:description" content="Runs COSMOS from signaling to metabolism.  This function uses CARNIVAL to find
+a subset of the prior knowledge network based on optimisation that (1)
 includes the most measured and input nodes and (2) which is in agreement with
 the data.  Use preprocess_COSMOS_signaling_to_metabolism to
-prepare inputs, measurements and prior knowledge network."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+prepare inputs, measurements and prior knowledge network."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -18,70 +15,46 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
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-      <ul class="navbar-nav"><li class="nav-item">
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>run COSMOS signaling to metabolism</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/run_COSMOS_signaling_to_metabolism.R" class="external-link"><code>R/run_COSMOS_signaling_to_metabolism.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/run_COSMOS_signaling_to_metabolism.R" class="external-link"><code>R/run_COSMOS_signaling_to_metabolism.R</code></a></small>
       <div class="d-none name"><code>run_COSMOS_signaling_to_metabolism.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>Runs COSMOS from signaling to metabolism.  This function uses CARNIVAL to find
-a subset of the prior knowledge network based on optimisation that (1) 
+a subset of the prior knowledge network based on optimisation that (1)
 includes the most measured and input nodes and (2) which is in agreement with
 the data.  Use <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> to
 prepare inputs, measurements and prior knowledge network.</p>
@@ -97,30 +70,28 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>data</dt>
+
+
+<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
 <dd><p><code><a href="cosmos_data.html">cosmos_data</a></code> object.  Use the
 <code><a href="preprocess_COSMOS_signaling_to_metabolism.html">preprocess_COSMOS_signaling_to_metabolism</a></code> function to create
 an instance.</p></dd>
 
 
-<dt>CARNIVAL_options</dt>
-<dd><p>List that controls the options of CARNIVAL. See 
+<dt id="arg-carnival-options">CARNIVAL_options<a class="anchor" aria-label="anchor" href="#arg-carnival-options"></a></dt>
+<dd><p>List that controls the options of CARNIVAL. See
 details in <code><a href="default_CARNIVAL_options.html">default_CARNIVAL_options</a></code>.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>List with the following elements:</p>
-<p></p>
-<dl><dt><code>weightedSIF</code></dt>
-<dd><p>The averaged networks found by 
-    optimization in a format of a Simple Interaction network, i.e. each row 
+    <p>List with the following elements:</p><dl><dt><code>weightedSIF</code></dt>
+<dd><p>The averaged networks found by
+    optimization in a format of a Simple Interaction network, i.e. each row
     codes an edge</p></dd>
 
     <dt><code>N_networks</code></dt>
-<dd><p>Number of solutions found by the 
+<dd><p>Number of solutions found by the
     optimization</p></dd>
 
     <dt><code>nodesAttributes</code></dt>
@@ -133,11 +104,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <dd><p>Node activity in each
     network</p></dd>
 
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code>,  
+    <div class="dont-index"><p><code><a href="preprocess_COSMOS_metabolism_to_signaling.html">preprocess_COSMOS_metabolism_to_signaling</a></code>,
   <code><a href="https://rdrr.io/pkg/CARNIVAL/man/runCARNIVAL.html" class="external-link">runCARNIVAL</a></code>, <code><a href="cosmos_data.html">cosmos_data</a></code></p></div>
     </div>
 
@@ -169,16 +140,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n69.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n69.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n69.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:41 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n69.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:39 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -188,14 +159,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression"</span>
@@ -210,16 +181,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign().</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers."</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- Start of the CARNIVAL pipeline ---</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Carnival flavour: vanilla</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Generating variables for lp problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Carnival flavour: vanilla</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Generating variables for lp problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: generating variables for lp problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving preprocessed data.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_42d24_06_2024n5.RData</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Generating formulation for LP problem</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: generating formulation for LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_40d15_07_2024n5.RData</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Generating formulation for LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: generating formulation for LP problem.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Saving LP file</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_42d24_06_2024n5.lp</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Solving LP problem</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_40d15_07_2024n5.lp</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Solving LP problem</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Parsing .lp file for lpSolve</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Rows: </span><span style="color: #0000BB;">882</span> <span style="font-weight: bold;">Columns: </span><span style="color: #0000BB;">1</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Column specification</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────</span></span>
@@ -229,19 +200,19 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Use `spec()` to retrieve the full column specification for this data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Specify the column types or set `show_col_types = FALSE` to quiet this message.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: parsing .lp file for lpSolve</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: solving LP problem.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Getting the solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: getting the solution matrix.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Exporting solution matrix</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 Done: exporting solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: solving LP problem.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Getting the solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: getting the solution matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Exporting solution matrix</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 Done: exporting solution matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Cleaning intermediate files</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Done: cleaning</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 08:13:42 24.06.2024 All tasks finished.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 09:38:40 15.07.2024 All tasks finished.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> --- End of the CARNIVAL pipeline --- </span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -250,14 +221,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
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-  
 
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diff --git a/reference/toy_RNA.html b/reference/toy_RNA.html
index d6d75d6..c1b2195 100644
--- a/reference/toy_RNA.html
+++ b/reference/toy_RNA.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><title>Toy Input Transcription Data Set — toy_RNA • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Transcription Data Set — toy_RNA"><meta property="og:description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Toy Input Transcription Data Set — toy_RNA • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Transcription Data Set — toy_RNA"><meta name="description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:description" content="This exemplary transcription data are the specific deregulated gene expression of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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-  <a class="nav-link" href="../news/index.html">Changelog</a>
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-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Toy Input Transcription Data Set</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/toy_RNA.R" class="external-link"><code>R/toy_RNA.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/toy_RNA.R" class="external-link"><code>R/toy_RNA.R</code></a></small>
       <div class="d-none name"><code>toy_RNA.Rd</code></div>
     </div>
 
@@ -91,7 +64,7 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular 
+    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular
   Systems Biology</em>. <b>17</b>, e9730.</p>
     </div>
 
@@ -101,7 +74,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -110,14 +83,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
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diff --git a/reference/toy_metabolic_input.html b/reference/toy_metabolic_input.html
index 7621c0d..a6b775d 100644
--- a/reference/toy_metabolic_input.html
+++ b/reference/toy_metabolic_input.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This metabolic data are a subset from the metabolic measurements of the 786-O cell line from the NCI60 dataset."><title>Toy Metabolic Input Data — toy_metabolic_input • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Metabolic Input Data — toy_metabolic_input"><meta property="og:description" content="This metabolic data are a subset from the metabolic measurements of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Toy Metabolic Input Data — toy_metabolic_input • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Metabolic Input Data — toy_metabolic_input"><meta name="description" content="This metabolic data are a subset from the metabolic measurements of the 786-O cell line from the NCI60 dataset."><meta property="og:description" content="This metabolic data are a subset from the metabolic measurements of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -10,64 +7,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
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+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
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-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Toy Metabolic Input Data</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/toy_metabolic_input.R" class="external-link"><code>R/toy_metabolic_input.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/toy_metabolic_input.R" class="external-link"><code>R/toy_metabolic_input.R</code></a></small>
       <div class="d-none name"><code>toy_metabolic_input.Rd</code></div>
     </div>
 
@@ -88,12 +61,12 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p>Subset of: 
+    <p>Subset of:
   <a href="https://github.com/saezlab/COSMOS_MSB/blob/main/data/metab_input_COSMOS.csv" class="external-link">https://github.com/saezlab/COSMOS_MSB/blob/main/data/metab_input_COSMOS.csv</a></p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular 
+    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular
   Systems Biology</em>. <b>17</b>, e9730.</p>
     </div>
 
@@ -103,7 +76,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -112,14 +85,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
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diff --git a/reference/toy_network.html b/reference/toy_network.html
index 69165ce..cd8cfc3 100644
--- a/reference/toy_network.html
+++ b/reference/toy_network.html
@@ -1,12 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This signaling network is the reduced COSMOS network solution obtained in the
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Toy Input Network — toy_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Network — toy_network"><meta name="description" content="This signaling network is the reduced COSMOS network solution obtained in the
 cosmos test on 786-O NCI60 data.  Here, this network solution is reused as an
-exemplary input prior knowledge network (PKN)."><title>Toy Input Network — toy_network • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Input Network — toy_network"><meta property="og:description" content="This signaling network is the reduced COSMOS network solution obtained in the
+exemplary input prior knowledge network (PKN)."><meta property="og:description" content="This signaling network is the reduced COSMOS network solution obtained in the
 cosmos test on 786-O NCI60 data.  Here, this network solution is reused as an
-exemplary input prior knowledge network (PKN)."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+exemplary input prior knowledge network (PKN)."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -14,64 +11,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
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-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
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-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Toy Input Network</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/toy_network.R" class="external-link"><code>R/toy_network.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/toy_network.R" class="external-link"><code>R/toy_network.R</code></a></small>
       <div class="d-none name"><code>toy_network.Rd</code></div>
     </div>
 
@@ -98,21 +71,21 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
     <dt><code>target</code></dt>
 <dd><p>Target node, either metabolite or protein</p></dd>
 
-  A detailed description of the identifier formatting can be found under 
+  A detailed description of the identifier formatting can be found under
   https://metapkn.omnipathdb.org/00__README.txt.
-  
+
 </dl></div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
     <p>The network data are available on github:
   <a href="https://github.com/saezlab/COSMOS_MSB/tree/main/results/COSMOS_result/COSMOS_res_session.RData" class="external-link">https://github.com/saezlab/COSMOS_MSB/tree/main/results/COSMOS_result/COSMOS_res_session.RData</a>.
-  The toy_network is the combined network of the COSMOS network solutions 
+  The toy_network is the combined network of the COSMOS network solutions
   CARNIVAL_Result2 and CARNIVAL_Result_rerun subsequently reduced to 19
   exemplary nodes.</p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular 
+    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular
   Systems Biology</em>. <b>17</b>, e9730.</p>
     </div>
 
@@ -122,7 +95,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -131,14 +104,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/toy_signaling_input.html b/reference/toy_signaling_input.html
index 37e646b..0838aa4 100644
--- a/reference/toy_signaling_input.html
+++ b/reference/toy_signaling_input.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This signaling data are a subset of the footprint-based signaling activity
-estimates of transcription factors of the 786-O cell line from the NCI60 dataset."><title>Toy Signaling Input — toy_signaling_input • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Signaling Input — toy_signaling_input"><meta property="og:description" content="This signaling data are a subset of the footprint-based signaling activity
-estimates of transcription factors of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Toy Signaling Input — toy_signaling_input • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Toy Signaling Input — toy_signaling_input"><meta name="description" content="This signaling data are a subset of the footprint-based signaling activity
+estimates of transcription factors of the 786-O cell line from the NCI60 dataset."><meta property="og:description" content="This signaling data are a subset of the footprint-based signaling activity
+estimates of transcription factors of the 786-O cell line from the NCI60 dataset."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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@@ -12,64 +9,40 @@
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 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
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+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
-    <span class="fab fa fab fa-twitter fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Toy Signaling Input</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/toy_signaling_input.R" class="external-link"><code>R/toy_signaling_input.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/toy_signaling_input.R" class="external-link"><code>R/toy_signaling_input.R</code></a></small>
       <div class="d-none name"><code>toy_signaling_input.Rd</code></div>
     </div>
 
@@ -91,12 +64,12 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p>Subset of: 
+    <p>Subset of:
   <a href="https://github.com/saezlab/COSMOS_MSB/blob/main/data/signaling_input_COSMOS.csv" class="external-link">https://github.com/saezlab/COSMOS_MSB/blob/main/data/signaling_input_COSMOS.csv</a></p>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular 
+    <p>Dugourd, A., Kuppe, C. and Sciacovelli, M. et. al. (2021) <em>Molecular
   Systems Biology</em>. <b>17</b>, e9730.</p>
     </div>
 
@@ -106,7 +79,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -115,14 +88,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/translate_column_HMDB.html b/reference/translate_column_HMDB.html
index 8de9644..bdc547b 100644
--- a/reference/translate_column_HMDB.html
+++ b/reference/translate_column_HMDB.html
@@ -1,10 +1,7 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function translates the values in a column using a provided Human Metabolome Database (HMDB) mapper vector.
-It modifies the input values by replacing certain prefixes and suffixes according to specific rules."><title>Translate Column Using HMDB Mapper — translate_column_HMDB • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Translate Column Using HMDB Mapper — translate_column_HMDB"><meta property="og:description" content="This function translates the values in a column using a provided Human Metabolome Database (HMDB) mapper vector.
-It modifies the input values by replacing certain prefixes and suffixes according to specific rules."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Translate Column Using HMDB Mapper — translate_column_HMDB • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Translate Column Using HMDB Mapper — translate_column_HMDB"><meta name="description" content="This function translates the values in a column using a provided Human Metabolome Database (HMDB) mapper vector.
+It modifies the input values by replacing certain prefixes and suffixes according to specific rules."><meta property="og:description" content="This function translates the values in a column using a provided Human Metabolome Database (HMDB) mapper vector.
+It modifies the input values by replacing certain prefixes and suffixes according to specific rules."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -12,64 +9,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a>
-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
-  </div>
-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
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-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
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-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
-  </a>
-</li>
+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Translate Column Using HMDB Mapper</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
       <div class="d-none name"><code>translate_column_HMDB.Rd</code></div>
     </div>
 
@@ -85,19 +58,19 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>my_column</dt>
+
+
+<dl><dt id="arg-my-column">my_column<a class="anchor" aria-label="anchor" href="#arg-my-column"></a></dt>
 <dd><p>A vector of values to be translated.</p></dd>
 
 
-<dt>HMDB_mapper_vec</dt>
+<dt id="arg-hmdb-mapper-vec">HMDB_mapper_vec<a class="anchor" aria-label="anchor" href="#arg-hmdb-mapper-vec"></a></dt>
 <dd><p>A named vector where the names are the original identifiers and the values are the corresponding HMDB identifiers.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A vector with the translated values.</p>
+    <p>A vector with the translated values.</p>
     </div>
 
     <div class="section level2">
@@ -111,7 +84,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -120,14 +93,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/translate_res.html b/reference/translate_res.html
index 00d2538..cb9d993 100644
--- a/reference/translate_res.html
+++ b/reference/translate_res.html
@@ -1,8 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="formats the network with readable names"><title>translate_res — translate_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="translate_res — translate_res"><meta property="og:description" content="formats the network with readable names"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>translate_res — translate_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="translate_res — translate_res"><meta name="description" content="formats the network with readable names"><meta property="og:description" content="formats the network with readable names"><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
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   gtag('js', new Date());
@@ -10,64 +7,40 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
-    
+
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
       <span class="navbar-toggler-icon"></span>
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
-  <a class="nav-link" href="../reference/index.html">Reference</a>
-</li>
+      <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
 <li class="nav-item dropdown">
-  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
-  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
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-    <a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a>
-    <a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a>
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-</li>
-<li class="nav-item">
-  <a class="nav-link" href="../news/index.html">Changelog</a>
-</li>
-      </ul><form class="form-inline my-2 my-lg-0" role="search">
-        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
-
-      <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="github">
-    <span class="fab fa fab fa-github fa-lg"></span>
-     
-  </a>
-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://twitter.com/saezlab">
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-     
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-</li>
-<li class="nav-item">
-  <a class="external-link nav-link" href="https://saezlab.org">
-    <span class="fas fa fas fa-university"></span>
-     
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+  <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
+  <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/MOFA_to_COSMOS.html">MOFA to COSMOS tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/NCI60_tutorial.html">NCI60 tutorial</a></li>
+    <li><a class="dropdown-item" href="../articles/tutorial.html">COSMOS-tutorial</a></li>
+  </ul></li>
+<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
+      </ul><ul class="navbar-nav"><li class="nav-item"><a class="external-link nav-link" href="https://github.com/saezlab/COSMOSR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://twitter.com/saezlab"><span class="fa fab fa-twitter fa-lg"></span></a></li>
+<li class="nav-item"><a class="external-link nav-link" href="https://saezlab.org"><span class="fa fas fa-university"></span></a></li>
       </ul></div>
 
-    
+
   </div>
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>translate_res</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/decoupleRnival.R" class="external-link"><code>R/decoupleRnival.R</code></a></small>
       <div class="d-none name"><code>translate_res.Rd</code></div>
     </div>
 
@@ -82,23 +55,23 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>SIF</dt>
+
+
+<dl><dt id="arg-sif">SIF<a class="anchor" aria-label="anchor" href="#arg-sif"></a></dt>
 <dd><p>result SIF of decoupleRnival pipeline</p></dd>
 
 
-<dt>ATT</dt>
+<dt id="arg-att">ATT<a class="anchor" aria-label="anchor" href="#arg-att"></a></dt>
 <dd><p>result ATT of decoupleRnival pipeline</p></dd>
 
 
-<dt>HMDB_mapper_vec</dt>
+<dt id="arg-hmdb-mapper-vec">HMDB_mapper_vec<a class="anchor" aria-label="anchor" href="#arg-hmdb-mapper-vec"></a></dt>
 <dd><p>a named vector with HMDB Ids as names and desired metabolite names as values.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>list with network and attribute tables.</p>
+    <p>list with network and attribute tables.</p>
     </div>
 
     <div class="section level2">
@@ -130,7 +103,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2 Enzyme863__GPX1 Metab__Oxiglutatione_c    1</span>
 </code></pre></div>
     </div>
-  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside></div>
 
 
@@ -139,14 +112,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
 </div>
 
     </footer></div>
 
-  
 
-  
+
+
 
   </body></html>
 
diff --git a/reference/wide_ulm_res.html b/reference/wide_ulm_res.html
index a8ffd46..170d82b 100644
--- a/reference/wide_ulm_res.html
+++ b/reference/wide_ulm_res.html
@@ -1,14 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function converts the results from a ULM analysis to a wide format data frame.
-The input is a data frame with columns for source, condition, and score. The output 
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Convert ULM Results to Wide Format — wide_ulm_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Convert ULM Results to Wide Format — wide_ulm_res"><meta name="description" content="This function converts the results from a ULM analysis to a wide format data frame.
+The input is a data frame with columns for source, condition, and score. The output
 is a data frame where each row represents a source and each column represents a condition,
-with the corresponding scores as values."><title>Convert ULM Results to Wide Format — wide_ulm_res • cosmosR</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Convert ULM Results to Wide Format — wide_ulm_res"><meta property="og:description" content="This function converts the results from a ULM analysis to a wide format data frame.
-The input is a data frame with columns for source, condition, and score. The output 
+with the corresponding scores as values."><meta property="og:description" content="This function converts the results from a ULM analysis to a wide format data frame.
+The input is a data frame with columns for source, condition, and score. The output
 is a data frame where each row represents a source and each column represents a condition,
-with the corresponding scores as values."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
+with the corresponding scores as values."><meta property="og:image" content="/logo.png"><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-PV71G2Q3SF"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
@@ -16,70 +13,46 @@
   gtag('config', 'G-PV71G2Q3SF');
 </script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
-    
 
-    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
-    
+
+    <nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
+
     <a class="navbar-brand me-2" href="../index.html">cosmosR</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.9.1</small>
 
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       <img src="../logo.png" class="logo" alt=""><h1>Convert ULM Results to Wide Format</h1>
-      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/HEAD/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/saezlab/COSMOSR/blob/master/R/support_decoupleR.R" class="external-link"><code>R/support_decoupleR.R</code></a></small>
       <div class="d-none name"><code>wide_ulm_res.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
     <p>This function converts the results from a ULM analysis to a wide format data frame.
-The input is a data frame with columns for source, condition, and score. The output 
+The input is a data frame with columns for source, condition, and score. The output
 is a data frame where each row represents a source and each column represents a condition,
 with the corresponding scores as values.</p>
     </div>
@@ -91,15 +64,15 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>ulm_result</dt>
+
+
+<dl><dt id="arg-ulm-result">ulm_result<a class="anchor" aria-label="anchor" href="#arg-ulm-result"></a></dt>
 <dd><p>A data frame representing the ULM results with columns: source, condition, and score.</p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
-    
-
-<p>A data frame in wide format where each row is a source and each column is a condition.</p>
+    <p>A data frame in wide format where each row is a source and each column is a condition.</p>
     </div>
 
     <div class="section level2">
@@ -114,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 </code></pre></div>
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 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/search.json b/search.json
index 86d2dfe..224f608 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"/articles/tutorial.html","id":"installation-and-dependency","dir":"Articles","previous_headings":"","what":"Installation and dependency","title":"COSMOS-tutorial","text":"COSMOS dependent CARNIVAL exhibiting signalling pathway optimisation. CARNIVAL requires interactive version IBM Cplex CBC-COIN solver network optimiser. IBM ILOG Cplex freely available Academic Initiative . CBC solver open source freely available user, significantly lower performance CPLEX. Obtain CBC executable directly usable cosmos . Alternatively small networks, users can rely freely available lpSolve R-package, automatically installed package. tutorial use lpSolve, strongly recommend obtain license CPLEX.","code":"# install from bioconductor if (!requireNamespace(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(\"cosmosR\")   # install the newest (development) version from GitHub # install.packages(\"remotes\") # install CARNIVAL from github  remotes::install_github(\"saezlab/CARNIVAL\") remotes::install_github(\"saezlab/cosmosR\")"},{"path":"/articles/tutorial.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"COSMOS-tutorial","text":"COSMOS (Causal Oriented Search Multi-Omic Space) method integrates phosphoproteomics, transcriptomics, metabolomics data sets. COSMOS leverages extensive prior knowledge signaling pathways, metabolic networks, gene regulation computational methods estimate activities transcription factors kinases well network-level causal reasoning. pipeline can provide mechanistic explanations experimental observations across multiple omic data sets. Essentially, COSMOS 3 main components: prior knowledge: goal COSMOS essentially connect various deregulation events together mechanistic hypotheses. mechanistic hypotheses basically known potential interactions molecular biology features, proteins metabolites. example interaction can activation MTOR AKT, EGFR canonical pathway. Thousands potential interaction can assembled together form large network interactions. networks thus called prior knowledge networks (PKN), summarize large amounts prior knowledge form network. context COSMOS interactions come Omnipath database, STICHdb recon3D reaction network. respect example interaction MTOR AKT, question usually asked presented given experimental context : MTOR can activate AKT general, interaction relevant experimental context? brings us second component COSMOS. data: Information deregulated transcription factors (TF), kinases/phosphophatases metabolites can extracted transcriptomic, phospho-proteomic metabolomic data respectively, using footprint analysis methods (see:https://github.com/saezlab/transcriptutorial (Especially chapter 4)). information can quite useful , characterize TFs kinases specifically deregulated cancer cells example. goal COSMOS find different deregulation events can connected together. Going back example MTOR AKT, know AKT can potentially activate MTOR, observe data AKT MTOR significantly activated cancer tissue compared healthy counterpart, reasonable chance interaction active cancer tissue ’m studying. problem data often contain information hundreds -regulated activities time, thousands potential interactions can potentially explain . order find optimal set interactions relevant explain deregulation observed data, algorithm needed. algorithm: problem described data part formulated integer linear optimisation problem. PKN data can abstracted large set integer variables operating together even larger set equations (see https://www.nature.com/articles/s41540-019-0118-z info). Given set fixed value variable (, subset known deregulation), need find values sets variable (corresponding proteins metabolites information data) can lead satisfying result. satisfying results context COSMOS represent sub-network interactions small possible coherently explaining many known deregulation possible. Thus, set equation mentioned earlier needs solved, using integer linear programming solver. solvers currently available COSMOS lpsolve, cbc cplex. general, CPLEX preferred CBC real case applications, lpsolve mainly used testing small networks sets measurements.","code":""},{"path":"/articles/tutorial.html","id":"tutorial-section-signaling-to-metabolism","dir":"Articles","previous_headings":"","what":"Tutorial section: signaling to metabolism","title":"COSMOS-tutorial","text":"First, load package part, can set options CARNIVAL run, timelimit min gap tolerance. user provide path CPLEX/cbc executable. can check CARNIVAL_options variable see possible options can adjusted example, use built-solver lpSolve. User aware lpSolve used TESTS. obtain meaningful results, best solver cplex, cbc possible. next section, prepare input run cosmosR. signaling inputs result footprint based TF kinase activity estimation. info TF activity estimation transcriptomic data, see:https://github.com/saezlab/transcriptutorial (Especially chapter 4) use toy PKN, see full meta PKN, can load data(meta_network). see meta_PKN assembled, see: https://github.com/saezlab/meta_PKN_BIGG.git metabolites prior knowledge network identified XMetab__HMDBid_compartment XMetab__BIGGid_compartment (example “Metab__HMDB0000190_c”). compartment code BIGG model standard (r, c, e, x, m, l, n, g). Thus first need map whatever identifier metabolite data one network. Genes identified gene symboles (signaling part network) Gene####__symbole (reaction network part network). maximum network depth define maximum number step downstream kinase/TF COSMOS look deregulated metabolites. Good first guess max depth around 4 6 (15 toy dataset) differential experession data used filter wrong TF-target interactions context pre-optimisation. list genes differential expression data also used reference define genes expressed (genes diff_expression_data considered expressed, genes diff_expression_data removed network). , CARNIVAL_options$timelimit set pre-optimisation. Indeed, “filter_tf_gene_interaction_by_optimization” parameter “preprocess_COSMOS_signaling_to_metabolism” function set TRUE, COSMOS can perform first optimisation run order generate preliminary solution network can used filtering incoherences TF activities downstream target expressions. part, can set options actual run, timelimit min gap tolerance. running time much higher pre-optimisation. can increase number threads use many available CPUs. cosmosR run. Finally, process results first cosmosR run, translate gene names metabolites name.","code":"library(cosmosR) CARNIVAL_options <- default_CARNIVAL_options(solver = \"lpSolve\")  # To use CBC # CARNIVAL_options <- default_CARNIVAL_options(solver = \"cbc\") # CARNIVAL_options$solverPath <- \"~/Documents/cbc\" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05  # To use CPLEX: # CARNIVAL_options <- default_CARNIVAL_options(solver = \"cplex\") # CARNIVAL_options$solverPath <- \"C:/Program Files/CPLEX_solver/cplex/bin/x64_win64/cplex.exe\" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05   CARNIVAL_options$timelimit <- 3600 data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,                                         signaling_data = toy_signaling_input,                                         metabolic_data = toy_metabolic_input,                                                       diff_expression_data = toy_RNA,                                                       maximum_network_depth = 15,                                                       remove_unexpressed_nodes = TRUE,                                                       CARNIVAL_options = CARNIVAL_options) ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" ## [1] \"COSMOS: removing unexpressed nodes from PKN...\" ## [1] \"COSMOS: 0 interactions removed\" ## [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" ## [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" ## [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" CARNIVAL_options$timelimit <- 14400 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for,                                                       CARNIVAL_options = CARNIVAL_options) ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" formated_result_for <- format_COSMOS_res(test_result_for)"},{"path":"/articles/tutorial.html","id":"tutorial-section-metabolism-to-signaling","dir":"Articles","previous_headings":"","what":"Tutorial section: metabolism to signaling","title":"COSMOS-tutorial","text":"run metabolism signaling part, need prepare inputs. Now correct time set pre-optimisation run, can prepare inputs. can run cosmosR connect metabolism signaling. running time usually needs longer, problem seems harder solve CPLEX. Finally can format result backward run well (forward run)","code":"CARNIVAL_options$timelimit <- 3600 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network,                                         signaling_data = toy_signaling_input,                                         metabolic_data = toy_metabolic_input,                                                        diff_expression_data = toy_RNA,                                                        maximum_network_depth = 15,                                                        remove_unexpressed_nodes = FALSE,                                                        CARNIVAL_options = CARNIVAL_options) ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" ## [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" ## [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" ## [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" CARNIVAL_options$timelimit <- 28800  test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back,                                                        CARNIVAL_options = CARNIVAL_options) ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" formated_result_back <- format_COSMOS_res(test_result_back)"},{"path":"/articles/tutorial.html","id":"tutorial-section-merge-forward-and-backward-networks-and-visualise-network","dir":"Articles","previous_headings":"","what":"Tutorial section: Merge forward and backward networks and visualise network","title":"COSMOS-tutorial","text":"simply take union forward backward runs create full network solution lopping signaling, gene-regulation metabolism. Since overlap result network forward backward run, may optionally want check node sign incoherent overlap two solutions. function generate dynamic network plot centered given node network solution, connecting measured nodes given range (7 steps). network can intepreted (purely illustrative, interaction may incorectly signed lpsolve can use positive interactions): network represents flow activities can connect MYC -regulation Glucitol (Sorbitol) accumulation. , NFKB1 can upregulate expression SLC2A1, turn transport glucose cytoplasm. increase transport glucose can lead glucose avlaible conversion glucitol AKR1A enzyme. Interestingly, glucitol now activator MAPK14, thus leading appearance positive feedback loop connecting MYC, glucitol MAPK14. important understand links hypothetical. come larger pool potential molecular interactions present multiple online databases compiled omnipath, STITCH recon metabolic network. exist literature interactions known potentially exists experimental contexts. Thus, COSMOS compile potential interactions together proposes coherent set can explain data hand. links however considered potential mechanistic connections, need confirmed experimentally. interactions can searched literature see disease experimental context shown relevant. Taken together, multiple interactions can help build biological story can guide underatanding underlying biology decide future experiments.","code":"full_sif <- as.data.frame(rbind(formated_result_for[[1]], formated_result_back[[1]])) full_sif <- full_sif[full_sif$Weight>0,] full_attributes <- as.data.frame(rbind(formated_result_for[[2]], formated_result_back[[2]]))  full_sif <- unique(full_sif) full_attributes <- unique(full_attributes) network_plot <- display_node_neighboorhood(central_node = 'Metab__D-Glucitol_c',                                             sif = full_sif,                                             att = full_attributes,                                             n = 7)  network_plot"},{"path":"/articles/tutorial.html","id":"tutorial-section-over-representation-analysis","dir":"Articles","previous_headings":"","what":"Tutorial section: Over Representation Analysis","title":"COSMOS-tutorial","text":"Often useful perform Representation Analysis (ORA) resulting nodes COSMOS network first analysis step get functional interpretation modeled signaling cascade. common way test whether selected genes (nodes) COSMOS solution network show statistically significant differences comparison prior-knowledge network (PKN). differentially expressed genes give information cellular processes deregulated proportions various pathways SIGNIFICANTLY different expected.way significant differences two biological conditions (e.g. cancer vs. normal tissue, treatment vs. untreated cells) can shown. Algorithms perform ORA implemented R packages like piano decoupleR. addition gene set collection algorithms require two different lists inputs: - nodes COSMOS solution network relate back input data (e.g. transcriptomics, proteomics, metabolomics, fluxomics, perturbations) - nodes (kinases, transcription factors, metabolites) prior-knowledge network (used background analysis) section show obtain two lists formated COSMOS result object. Now forward backward sets can used ORA analysis.","code":"sif_forward = formated_result_for[[1]] att_forward = formated_result_for[[2]] nodes_ORA = extract_nodes_for_ORA(     sif = sif_forward,      att = att_forward) sessionInfo() ## R version 4.4.0 (2024-04-24) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] cosmosR_1.9.1 ##  ## loaded via a namespace (and not attached): ##  [1] bcellViper_1.40.0   sass_0.4.9          utf8_1.2.4          ##  [4] generics_0.1.3      tidyr_1.3.1         lpSolve_5.6.20      ##  [7] stringi_1.8.4       lattice_0.22-6      hms_1.1.3           ## [10] digest_0.6.35       magrittr_2.0.3      evaluate_0.24.0     ## [13] grid_4.4.0          fastmap_1.2.0       jsonlite_1.8.8      ## [16] Matrix_1.7-0        progress_1.2.3      purrr_1.0.2         ## [19] fansi_1.0.6         codetools_0.2-20    textshaping_0.4.0   ## [22] jquerylib_0.1.4     cli_3.6.3           rlang_1.1.4         ## [25] decoupleR_2.10.0    crayon_1.5.3        visNetwork_2.1.2    ## [28] parallelly_1.37.1   bit64_4.0.5         withr_3.0.0         ## [31] cachem_1.1.0        yaml_2.3.8          tools_4.4.0         ## [34] parallel_4.4.0      tzdb_0.4.0          BiocParallel_1.38.0 ## [37] memoise_2.0.1       dplyr_1.1.4         vctrs_0.6.5         ## [40] R6_2.5.1            lifecycle_1.0.4     stringr_1.5.1       ## [43] bit_4.0.5           fs_1.6.4            htmlwidgets_1.6.4   ## [46] vroom_1.6.5         ragg_1.3.2          pkgconfig_2.0.3     ## [49] desc_1.4.3          pkgdown_2.0.9       pillar_1.9.0        ## [52] bslib_0.7.0         glue_1.7.0          systemfonts_1.1.0   ## [55] xfun_0.45           tibble_3.2.1        tidyselect_1.2.1    ## [58] CARNIVAL_2.14.0     knitr_1.47          dorothea_1.16.0     ## [61] rjson_0.2.21        igraph_2.0.3        htmltools_0.5.8.1   ## [64] rmarkdown_2.27      readr_2.1.5         compiler_4.4.0      ## [67] prettyunits_1.2.0"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Aurélien Dugourd. Author. Attila Gabor. Maintainer. Katharina Zirngibl. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B. Emdal, Vitor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric. M. J. Bindels, Ana S. H. Costa, Abel sousa, Pedro Beltrao, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez. 'Causal integration multi-omics data prior knowledge generate mechanistic hypotheses.' Molecular Systems Biology. 2021.","code":"@Article{,   author = {Aurelien Dugourd and Christoph Kuppe and Marco Sciacovelli and Enio Gjerga and Attila Gabor and Kristina B. Embdal and Vitor Vieira and Dorte B. Bekker-Jensen and Jennifer Kranz and Eric M. J. Bindels and Ana S. H. Costa and Abel Sousa and Pedro Beltrao and Jesper V Olsen and Christian Frezza and Rafael Kramann and Julio Saez-Rodriguez},   title = {Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses},   journal = {Molecular Systems Biology},   year = {2021}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"COSMOS (Causal Oriented Search Multi-Omic Space) method integrates phosphoproteomics, transcriptomics, metabolomics data sets. COSMOS leverages extensive prior knowledge signaling pathways, metabolic networks, gene regulation computational methods estimate activities transcription factors kinases well network-level causal reasoning. pipeline can provide mechanistic explanations experimental observations across multiple omic data sets.  COSMOS finds coherent subnetwork causally connecting many deregulated TFs, kinases/phosphatases metabolites possible. subnetwork extracted novel integrated PKN (available ) spanning signaling, transcriptional regulation metabolism. Transcription factors activities inferred gene expression decoupleR. Kinase activities inferred phosphoproteomic kinase/substrate network Omnipath, meta resource protein-protein. scripts generate current network can found : https://github.com/saezlab/meta_PKN_BIGG. can also use COSMOS don’t metabolomic data, connect TF activities (transcriptomic) kinase activities (phosphoproteomic) exmaple !","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"R >= 4.1 required don’t R 4.1, can also clone github repository machine, create new R project R studio cosmosR folder, change R version R version DESCRIPTION file install devtools:install() 4.1 advised case.","code":"# install from bioconductor if (!requireNamespace(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"cosmosR\")  # We advise to instal from github to get the latest version of the tool. if (!requireNamespace(\"devtools\", quietly = TRUE))     install.packages(\"devtools\")      devtools::install_github(\"saezlab/cosmosR\")"},{"path":"/index.html","id":"tutorial-to-use-mofa-nad-cosmos","dir":"","previous_headings":"","what":"tutorial to use MOFA nad COSMOS","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"[](https://github.com/saezlab/Factor_COSMOS can find extensive tutorial showing use MOFA COSMOS NCI60 dataset. extensive tutorial, wish get quicker plug play introduction COSMOS, see .","code":""},{"path":"/index.html","id":"tutorial-nci60-playground","dir":"","previous_headings":"","what":"Tutorial (NCI60 playground)","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"made repository contains pre-processed inputs example script use cosmos NCI60 RNA+metabolomic datasets. can find repository [](https://github.com/saezlab/COSMOS_basic.","code":""},{"path":"/index.html","id":"access","dir":"","previous_headings":"","what":"Access","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"meta PKN used biorXiv version COSMOS available . updated meta PKN available package (using data(meta_network) R)","code":""},{"path":"/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"use cosmosR research please cite original publication: Dugourd , Kuppe C, Sciacovelli M, Gjerga E, Gabor , Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Jesper V Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez et al (2021) Causal integration multi-omics data prior knowledge generate mechanistic hypotheses. Mol Syst Biol 17: e9730","code":""},{"path":"/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"code distributed GNU General Public License v3.0. meta PKN distributed Attribution-NonCommercial 4.0 International (CC--NC 4.0) License.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Input Transcription Data Set — HMDB_mapper_vec","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"exemplary transcription data specific deregulated gene expression 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"","code":"data(HMDB_mapper_vec)"},{"path":"/reference/HMDB_mapper_vec.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"object class “character” containing marching HMDB metabolite IDs coresponding metabolite names.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"https://bioconductor.org/packages/release/data/annotation/html/metaboliteIDmapping.html","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"","code":"data(HMDB_mapper_vec)"},{"path":"/reference/compress_same_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Compress Network by Merging Nodes with Identical Children — compress_same_children","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"function compresses network merging nodes children. input network represented data frame three columns: source, target, sign interaction. function returns list containing compressed network, node signatures, duplicated signatures.","code":""},{"path":"/reference/compress_same_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"","code":"compress_same_children(df, sig_input, metab_input)"},{"path":"/reference/compress_same_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"df data frame representing network three columns: source, target, sign interaction. sig_input list input node signatures considered merging process. metab_input list input metabolic signatures considered merging process.","code":""},{"path":"/reference/compress_same_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"list containing following elements: compressed_network data frame representing compressed network. node_signatures list signatures nodes network merging process. duplicated_signatures list duplicated signatures network merging process.","code":""},{"path":"/reference/compress_same_children.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"","code":"# Create a sample network df <- data.frame(source = c(\"A\", \"A\", \"B\", \"B\"),                  target = c(\"C\", \"D\", \"C\", \"D\"),                  sign_of_interaction = c(1, 1, 1, 1))  # Define input node and metabolic signatures sig_input <- list() metab_input <- list()  # Compress the network result <- compress_same_children(df, sig_input, metab_input) compressed_network <- result$compressed_network"},{"path":"/reference/cosmos_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Cosmos Data — cosmos_data","title":"Create Cosmos Data — cosmos_data","text":"S3 class combines required data comprehensive list.  Use  preprocess_COSMOS_signaling_to_metabolism  preprocess_COSMOS_metabolism_to_signaling create instance.","code":""},{"path":"/reference/cosmos_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Cosmos Data — cosmos_data","text":"","code":"cosmos_data(   meta_network,   tf_regulon = NULL,   signaling_data,   metabolic_data,   expression_data,   verbose = TRUE )"},{"path":"/reference/cosmos_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Cosmos Data — cosmos_data","text":"meta_network Prior knowledge network (PKN).  default COSMOS use PKN derived Omnipath, STITCHdb Recon3D.  See details data  meta_network. tf_regulon Collection transcription factor - target interactions. default collection dorothea can obtained  load_tf_regulon_dorothea function. signaling_data Numerical vector, names signaling nodes  PKN values {1, 0, -1}.  Continuous data  discretized using sign function. metabolic_data Numerical vector, names metabolic nodes  PKN values continuous values represents log2 fold change  t-values differential analysis.  values compared  simulation results (simulated nodes can take value -1, 0 1). expression_data Numerical vector represents results  differential gene expression analysis. Names gene names using EntrezID  starting X values log fold change t-values. Genes  NA values considered none expressed removed TF-gene expression interactions. verbose (default: TRUE) Reports details cosmos_data object.","code":""},{"path":"/reference/cosmos_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Cosmos Data — cosmos_data","text":"cosmos data class instance.","code":""},{"path":"/reference/createLinearColors.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Linear Colors Based on Numeric Input — createLinearColors","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"function generates gradient colors based provided numeric values. colors can adjusted include zero configurable specified maximum custom color palette.","code":""},{"path":"/reference/createLinearColors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"","code":"createLinearColors(   numbers,   withZero = T,   maximum = 100,   my_colors = c(\"royalblue3\", \"white\", \"red\") )"},{"path":"/reference/createLinearColors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"numbers numeric vector color gradient generated. withZero logical value indicating whether zero included color gradient. Default TRUE. maximum integer specifying maximum number colors generated gradient. Default 100. my_colors character vector length three specifying colors used gradient. Default c(\"royalblue3\", \"white\", \"red\").","code":""},{"path":"/reference/createLinearColors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"character vector colors representing gradient based input numeric values.","code":""},{"path":"/reference/createLinearColors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"","code":"# Generate colors for a set of numbers including zero numbers <- c(-50, -20, 0, 20, 50) colors <- createLinearColors(numbers, withZero = TRUE, maximum = 100)"},{"path":"/reference/decompress_moon_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompress Moon Result — decompress_moon_result","title":"Decompress Moon Result — decompress_moon_result","text":"function decompresses results obtained moon analysis incorporating  node signatures handling duplicated parents. merges details  provided meta network data returns comprehensive data frame.","code":""},{"path":"/reference/decompress_moon_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompress Moon Result — decompress_moon_result","text":"","code":"decompress_moon_result(moon_res, meta_network_compressed_list, meta_network)"},{"path":"/reference/decompress_moon_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompress Moon Result — decompress_moon_result","text":"moon_res data frame containing results moon analysis. meta_network_compressed_list list containing compressed meta network details,  including node signatures duplicated parents. meta_network data frame representing original meta network.","code":""},{"path":"/reference/decompress_moon_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompress Moon Result — decompress_moon_result","text":"data frame merges moon analysis results meta network data,         including additional details node signatures handling duplicated parents.","code":""},{"path":"/reference/decompress_moon_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompress Moon Result — decompress_moon_result","text":"","code":"# Example usage (requires appropriate data structures for moon_res,  # meta_network_compressed_list, and meta_network) # decompressed_result <- decompress_moon_result(moon_res, meta_network_compressed_list, meta_network)"},{"path":"/reference/decompress_solution_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompress Solution Network — decompress_solution_network","title":"Decompress Solution Network — decompress_solution_network","text":"function decompresses solution network mapping node signatures back original identifiers. input formatted solution network, meta network, node signatures, duplicated parents. function returns list containing decompressed solution network attribute table.","code":""},{"path":"/reference/decompress_solution_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompress Solution Network — decompress_solution_network","text":"","code":"decompress_solution_network(   formatted_res,   meta_network,   node_signatures,   duplicated_parents )"},{"path":"/reference/decompress_solution_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompress Solution Network — decompress_solution_network","text":"formatted_res list containing solution network attribute table. meta_network data frame representing meta network. node_signatures list node signatures. duplicated_parents list duplicated parents compression process.","code":""},{"path":"/reference/decompress_solution_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompress Solution Network — decompress_solution_network","text":"list containing following elements: SIF data frame representing decompressed solution network. ATT data frame containing attributes decompressed solution network.","code":""},{"path":"/reference/decompress_solution_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompress Solution Network — decompress_solution_network","text":"","code":"# Create a sample formatted_res formatted_res <- list(   SIF = data.frame(source = c(\"parent_of_D1\", \"D\"),                    target = c(\"D\", \"F\"),                    interaction = c(1, 1),                    Weight = c(1, 1)),   ATT = data.frame(Nodes = c(\"parent_of_D1\", \"D\", \"F\"),                    NodeType = c(\"\",\"\",\"\"),                    ZeroAct = c(0,0,0),                    UpAct = c(1,1,1),                    DownAct = c(0,0,0),                    AvgAct = c(1,1,1),                    measured = c(0,0,0),                    Activity = c(1,1,1)) )  # Create a sample meta_network meta_network <- data.frame(source = c(\"A\", \"B\", \"D\"),                            target = c(\"D\", \"D\", \"F\"),                            interaction_type = c(1, 1, 1))  # Define node_signatures and duplicated_parents node_signatures <- list(\"A\" = \"parent_of_D1\",\"B\" = \"parent_of_D1\",\"D\" = \"parent_F1\") duplicated_parents <- c(\"A\" = \"parent_of_D1\",\"B\" = \"parent_of_D1\")  # Decompress the solution network result <- decompress_solution_network(formatted_res, meta_network, node_signatures, duplicated_parents) decompressed_network <- result[[1]] attribute_table <- result[[2]]"},{"path":"/reference/decoupleRnival.html","id":null,"dir":"Reference","previous_headings":"","what":"DecoupleRnival — decoupleRnival","title":"DecoupleRnival — decoupleRnival","text":"Iteratively propagate downstream input activity signed directed network using weighted mean enrichment score decoupleR package","code":""},{"path":"/reference/decoupleRnival.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DecoupleRnival — decoupleRnival","text":"","code":"decoupleRnival(   upstream_input = NULL,   downstream_input,   meta_network,   n_layers,   n_perm = 1000,   downstream_cutoff = 0,   statistic = \"norm_wmean\" )"},{"path":"/reference/decoupleRnival.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DecoupleRnival — decoupleRnival","text":"upstream_input named vector up_stream nodes corresponding activity. downstream_input named vector down_stream nodes corresponding activity. meta_network network data frame containing signed directed prior knowledge molecular interactions. n_layers number layers propagated upstream. n_perm number permutations use decoupleR's algorithm. downstream_cutoff downstream measurments included given threshold statistic decoupleR stat consider: \"wmean\", \"norm_wmean\", \"ulm\"","code":""},{"path":"/reference/decoupleRnival.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DecoupleRnival — decoupleRnival","text":"data frame containing score nodes upstream  downstream input based iterative propagation","code":""},{"path":"/reference/decoupleRnival.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DecoupleRnival — decoupleRnival","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"C\", \"D\", \"E\", \"D\", \"B\", \"A\"),   sign = c(1, -1, -1, 1, -1, -1, 1) )  # Run the function with the example input data result <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\" #> [1] 2  # View the results print(result) #>   source    score #> 1      B -1.05659 #> D      D  2.00000 #> E      E -1.50000"},{"path":"/reference/default_CARNIVAL_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Setting Default CARNIVAL Options — default_CARNIVAL_options","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"Returns default CARNIVAL options list.  can modify elements list use argument run_COSMOS_metabolism_to_signaling   run_COSMOS_signaling_to_metabolism. choose CPLEX CBC, must modify solverPath field point  CPLEX/CBC executable (See Details).","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"","code":"default_CARNIVAL_options(solver = NULL)"},{"path":"/reference/default_CARNIVAL_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"solver one `cplex` (recommended, require 3rd party tool), `cbc` (also require 3rd party tool) `lpSolve` (small networks)","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"returns list possible options implemented CARNIVAL. see documentation runCARNIVAL.","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"COSMOS dependent CARNIVAL exhibiting signalling pathway optimisation. CARNIVAL requires interactive version IBM Cplex, Gurobi CBC-COIN solver  network optimiser. IBM ILOG Cplex freely available Academic Initiative . Gurobi license also free academics, request license following instructions .  CBC solver open source freely available user, significantly lower performance CPLEX  Gurobi. Obtain CBC executable directly usable cosmos . Alternatively small networks, users can rely freely available   lpSolve R-package,  automatically installed package.","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"","code":"# load and change default options:  my_options = default_CARNIVAL_options(solver = \"cplex\")   my_options$solverPath = \"/Applications/CPLEX_Studio128/cplex/bin/x86-64_osx/cplex\" my_options$threads = 2 my_options$timelimit = 3600*15"},{"path":"/reference/display_node_neighboorhood.html","id":null,"dir":"Reference","previous_headings":"","what":"display_node_neighboorhood — display_node_neighboorhood","title":"display_node_neighboorhood — display_node_neighboorhood","text":"display input measurements within n steps given set nodes","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"display_node_neighboorhood — display_node_neighboorhood","text":"","code":"display_node_neighboorhood(central_node, sif, att, n = 100)"},{"path":"/reference/display_node_neighboorhood.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"display_node_neighboorhood — display_node_neighboorhood","text":"central_node character character vector; node ID(s) around  network branched untill meansurments input reached sif df; COSMOS network solution sif format like first list element returned format_cosmos_res function att df; attributes nodes COMSOS network solution like  second list element returned format_cosmos_res function n numeric; maximum number steps network look inputs  measurments","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"display_node_neighboorhood — display_node_neighboorhood","text":"visnetwork object","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"display_node_neighboorhood — display_node_neighboorhood","text":"","code":"CARNIVAL_options <- cosmosR::default_CARNIVAL_options(\"lpSolve\") data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:33 24.06.2024 Carnival flavour: vanilla #> 08:13:33 24.06.2024 Generating variables for lp problem #> 08:13:33 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_33d24_06_2024n45.RData #> 08:13:33 24.06.2024 Generating formulation for LP problem #> 08:13:33 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_33d24_06_2024n45.lp #> 08:13:33 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:34 24.06.2024 Done: solving LP problem. #> 08:13:34 24.06.2024 Getting the solution matrix #> 08:13:34 24.06.2024 Done: getting the solution matrix. #> 08:13:34 24.06.2024 Exporting solution matrix #> 08:13:34 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:34 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:34 24.06.2024 Carnival flavour: vanilla #> 08:13:34 24.06.2024 Generating variables for lp problem #> 08:13:34 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_34d24_06_2024n23.RData #> 08:13:34 24.06.2024 Generating formulation for LP problem #> 08:13:34 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_34d24_06_2024n23.lp #> 08:13:34 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:34 24.06.2024 Done: solving LP problem. #> 08:13:34 24.06.2024 Getting the solution matrix #> 08:13:34 24.06.2024 Done: getting the solution matrix. #> 08:13:34 24.06.2024 Exporting solution matrix #> 08:13:34 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:34 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  test_result_for <- format_COSMOS_res(test_result_for) network_plot <- display_node_neighboorhood(central_node = 'MYC', sif = test_result_for[[1]], att = test_result_for[[2]], n = 7) #> Warning: At vendor/cigraph/src/paths/unweighted.c:444 : Couldn't reach some vertices. network_plot  {\"x\":{\"nodes\":{\"id\":[\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"FGFR1\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucitol_c\",\"Metab__D-Glucose_c\",\"Metab__L-Lactic acid_c\",\"SLC2A1\"],\"NodeType\":[\"\",\"\",\"\",\"\",\"\",\"\",\"P\",\"M\",\"\",\"M\",\"\"],\"ZeroAct\":[0,0,0,0,0,0,0,0,0,0,0],\"UpAct\":[1,1,1,1,1,1,1,1,1,1,1],\"DownAct\":[0,0,0,0,0,0,0,0,0,0,0],\"AvgAct\":[1,1,1,1,1,1,1,1,1,1,1],\"measured\":[0,0,0,0,0,0,1,1,0,1,0],\"Activity\":[1,1,1,1,1,1,1,1,1,1,1],\"label\":[\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"FGFR1\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucitol_c\",\"Metab__D-Glucose_c\",\"Metab__L-Lactic acid_c\",\"SLC2A1\"],\"color\":[\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\"],\"shape\":[\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\"],\"shadow\":[false,false,false,false,false,false,true,true,false,true,false]},\"edges\":{\"from\":[\"MAPK14\",\"Metab__D-Glucitol_c\",\"FGFR1\",\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucose_c\",\"SLC2A1\"],\"to\":[\"MYC\",\"MAPK14\",\"LDHA\",\"Metab__D-Glucitol_c\",\"Metab__L-Lactic acid_c\",\"Metab__D-Glucose_c\",\"Enzyme7338__LDHB_LDHA_reverse\",\"FGFR1\",\"SLC2A1\",\"Enzyme1338__AKR1A1\",\"Enzyme9049__SLC2A1_reverse\"],\"sign\":[1,1,1,1,1,1,1,-1,1,1,1],\"weigth\":[1,1,1,1,1,1,1,0,1,1,1],\"color\":[\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\"],\"arrows.to.type\":[\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"circle\",\"arrow\",\"arrow\",\"arrow\"],\"enabled\":[true,true,true,true,true,true,true,true,true,true,true],\"scaleFactor\":[1,1,1,1,1,1,1,1,1,1,1]},\"nodesToDataframe\":true,\"edgesToDataframe\":true,\"options\":{\"width\":\"100%\",\"height\":\"100%\",\"nodes\":{\"shape\":\"dot\"},\"manipulation\":{\"enabled\":false}},\"groups\":null,\"width\":1600,\"height\":1600,\"idselection\":{\"enabled\":true,\"style\":\"width: 200px; height: 26px;\\n                                              background: #f8f8f8;\\n                                              color: darkblue;\\n                                              border:none;\\n                                              outline:none;\",\"useLabels\":true,\"main\":\"Select by id\"},\"byselection\":{\"enabled\":false,\"style\":\"width: 150px; height: 26px\",\"multiple\":false,\"hideColor\":\"rgba(200,200,200,0.5)\",\"highlight\":false},\"main\":null,\"submain\":null,\"footer\":null,\"background\":\"rgba(0, 0, 0, 0)\",\"highlight\":{\"enabled\":true,\"hoverNearest\":false,\"degree\":1,\"algorithm\":\"all\",\"hideColor\":\"rgba(200,200,200,0.5)\",\"labelOnly\":true},\"collapse\":{\"enabled\":false,\"fit\":false,\"resetHighlight\":true,\"clusterOptions\":null,\"keepCoord\":true,\"labelSuffix\":\"(cluster)\"}},\"evals\":[],\"jsHooks\":[]}"},{"path":"/reference/extract_nodes_for_ORA.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"Function extract nodes appear COSMOS output network background genes (genes present prior knowledge network)","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"","code":"extract_nodes_for_ORA(sif, att)"},{"path":"/reference/extract_nodes_for_ORA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"sif df; COSMOS network solution sif format like first list element returned format_cosmos_res function att df; attributes nodes COMSOS network solution like  second list element returned format_cosmos_res function","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"List 2 objects: success background genes","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"","code":"CARNIVAL_options <- cosmosR::default_CARNIVAL_options(\"lpSolve\") data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:35 24.06.2024 Carnival flavour: vanilla #> 08:13:35 24.06.2024 Generating variables for lp problem #> 08:13:35 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_35d24_06_2024n76.RData #> 08:13:35 24.06.2024 Generating formulation for LP problem #> 08:13:35 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_35d24_06_2024n76.lp #> 08:13:35 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:35 24.06.2024 Done: solving LP problem. #> 08:13:35 24.06.2024 Getting the solution matrix #> 08:13:35 24.06.2024 Done: getting the solution matrix. #> 08:13:35 24.06.2024 Exporting solution matrix #> 08:13:35 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:35 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:35 24.06.2024 Carnival flavour: vanilla #> 08:13:35 24.06.2024 Generating variables for lp problem #> 08:13:35 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_35d24_06_2024n63.RData #> 08:13:35 24.06.2024 Generating formulation for LP problem #> 08:13:35 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_35d24_06_2024n63.lp #> 08:13:35 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:36 24.06.2024 Done: solving LP problem. #> 08:13:36 24.06.2024 Getting the solution matrix #> 08:13:36 24.06.2024 Done: getting the solution matrix. #> 08:13:36 24.06.2024 Exporting solution matrix #> 08:13:36 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:36 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  test_result_for <- format_COSMOS_res(test_result_for) extreacted_nodes <- extract_nodes_for_ORA( sif = test_result_for[[1]], att = test_result_for[[2]] )"},{"path":"/reference/filter_incohrent_TF_target.html","id":null,"dir":"Reference","previous_headings":"","what":"filter_incohrent_TF_target — filter_incohrent_TF_target","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"Filters incoherent target genes regulatory network based decoupling analysis upstream downstream gene expression.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"","code":"filter_incohrent_TF_target(   decouplRnival_res,   TF_reg_net,   meta_network,   RNA_input )"},{"path":"/reference/filter_incohrent_TF_target.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"decouplRnival_res data frame resulting decoupleRnival function. TF_reg_net data frame containing prior knowledge transcription factor (TF) regulatory interactions. meta_network network data frame containing signed directed prior knowledge molecular interactions. RNA_input named vector containing differential gene expression data.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"network data frame containing genes incoherently regulated TFs.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"D\", \"D\", \"E\", \"D\", \"B\", \"A\"),   interaction = c(-1, 1, -1, 1, -1, -1, 1) ) RNA_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 5, \"D\" = -0.7, \"E\" = -0.3)  TF_reg_net <- data.frame( source = c(\"B\"), target = c(\"D\"), mor = c(-1) )  # Run the decoupleRnival function to get the upstream influence scores upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\"  filtered_network <- filter_incohrent_TF_target(upstream_scores, TF_reg_net, meta_network, RNA_input)  print(filtered_network) #>   source target interaction #> 1      A      B          -1 #> 2      A      D           1 #> 4      C      E           1 #> 5      C      D          -1 #> 6      D      B          -1 #> 7      E      A           1"},{"path":"/reference/format_COSMOS_res.html","id":null,"dir":"Reference","previous_headings":"","what":"format_COSMOS_res — format_COSMOS_res","title":"format_COSMOS_res — format_COSMOS_res","text":"formats network readable names","code":""},{"path":"/reference/format_COSMOS_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"format_COSMOS_res — format_COSMOS_res","text":"","code":"format_COSMOS_res(cosmos_res, metab_mapping = NULL)"},{"path":"/reference/format_COSMOS_res.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"format_COSMOS_res — format_COSMOS_res","text":"cosmos_res results COSMOS run metab_mapping named vector HMDB Ids names desired metabolite names values.","code":""},{"path":"/reference/format_COSMOS_res.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"format_COSMOS_res — format_COSMOS_res","text":"list network attribute tables.","code":""},{"path":"/reference/format_LR_ressource.html","id":null,"dir":"Reference","previous_headings":"","what":"Format Ligand-Receptor Resource — format_LR_ressource","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"function formats ligand-receptor resource creating gene set source-target pairs, converting long format, adding default values 'mor' 'likelihood'.","code":""},{"path":"/reference/format_LR_ressource.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"","code":"format_LR_ressource(ligrec_ressource)"},{"path":"/reference/format_LR_ressource.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"ligrec_ressource data frame representing ligand-receptor resource columns source target gene symbols.","code":""},{"path":"/reference/format_LR_ressource.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"data frame containing formatted ligand-receptor gene set columns: gene gene symbol ligand-receptor pairs. set set identifier combining source target gene symbols. mor Default value set 1 entries. likelihood Default value set 1 entries.","code":""},{"path":"/reference/format_LR_ressource.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"","code":"# Create a sample ligand-receptor resource ligrec_ressource <- data.frame(source_genesymbol = c(\"L1\", \"L2\"),                                target_genesymbol = c(\"R1\", \"R2\"))  # Format the ligand-receptor resource formatted_geneset <- format_LR_ressource(ligrec_ressource)"},{"path":"/reference/get_moon_scoring_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Moon Scoring Network — get_moon_scoring_network","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"function analyzes given meta network based moon scores upstream node.  filters processes network controlling observing neighbours  according specified parameters. function returns list containing filtered  network updated moon scores.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"","code":"get_moon_scoring_network(   upstream_node,   meta_network,   moon_scores,   keep_upstream_node_peers = F )"},{"path":"/reference/get_moon_scoring_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"upstream_node node network analysis starts. meta_network complete network data. moon_scores Scores associated node network. keep_upstream_node_peers Logical; whether keep peers upstream node. Default FALSE.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"list two elements:    - `SIF`: data frame representing filtered meta network.   - `ATT`: data frame representing updated moon scores.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"","code":"# Example usage (requires appropriate data structures for meta_network and moon_scores) # result <- get_moon_scoring_network(upstream_node, meta_network, moon_scores)"},{"path":"/reference/gmt_to_dataframe.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert gmt file to data frame — gmt_to_dataframe","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"function designed convert gmt file (gene set file MSigDB) two column data frame first column corresponds omic features (genes) second column associated terms (pathway gene belongs ). One gene can belong several pathways.","code":""},{"path":"/reference/gmt_to_dataframe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"","code":"gmt_to_dataframe(gmtfile)"},{"path":"/reference/gmt_to_dataframe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"gmtfile full path name gmt file converted","code":""},{"path":"/reference/gmt_to_dataframe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"two column data frame first column corresponds omic features second column associated terms (pathways).","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":null,"dir":"Reference","previous_headings":"","what":"load transcription factor regulon — load_tf_regulon_dorothea","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"load transcription factors DOROTHEA package converts  gene symbols EntrezID using org.Hs.eg.db","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"","code":"load_tf_regulon_dorothea(confidence = c(\"A\", \"B\", \"C\"))"},{"path":"/reference/load_tf_regulon_dorothea.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"confidence strong vector (default: c(\"\",\"B\",\"C\")). Subset {, B,  C, D, E}. See `dorothea` meaning confidence levels.  package details.","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"returns PKN form data table. row interaction. Columns names : - `tf` transcription factor - `confidence` class confidence - `target` target gene - `sign` indicates interaction (1) -regulation (-1).","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"","code":"load_tf_regulon_dorothea() #> # A tibble: 13,223 × 3 #>    tf    target    sign #>    <chr> <chr>    <dbl> #>  1 AHR   CYP1A1       1 #>  2 AHR   CYP1A2       1 #>  3 AHR   CYP1B1       1 #>  4 AHR   FOS          1 #>  5 AHR   MYC          1 #>  6 AHR   UGT1A6       1 #>  7 AHR   ASAP1        1 #>  8 AHR   ERG          1 #>  9 AHR   VGLL4        1 #> 10 AHR   ARHGAP15     1 #> # ℹ 13,213 more rows"},{"path":"/reference/make_heatmap_color_palette.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Heatmap Color Palette — make_heatmap_color_palette","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"function generates color palette suitable heatmaps based values matrix. uses `createLinearColors` function generate separate color gradients positive negative values.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"","code":"make_heatmap_color_palette(my_matrix)"},{"path":"/reference/make_heatmap_color_palette.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"my_matrix numeric matrix heatmap color palette generated.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"character vector colors representing heatmap color palette based input matrix values.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"","code":"# Create a sample matrix my_matrix <- matrix(c(-3, -1, 0, 1, 3), nrow = 1)  # Generate heatmap color palette heatmap_palette <- make_heatmap_color_palette(my_matrix)"},{"path":"/reference/meta_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Meta Prior Knowledge Network — meta_network","title":"Meta Prior Knowledge Network — meta_network","text":"Comprehensive Prior Knowledge Network (PKN), combines signaling metabolic interaction networks.  network constructed using Recon3D  STITCH metabolic networks well signaling network OmniPath.","code":""},{"path":"/reference/meta_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Meta Prior Knowledge Network — meta_network","text":"","code":"data(meta_network)"},{"path":"/reference/meta_network.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Meta Prior Knowledge Network — meta_network","text":"object class “tibble” 117065 rows   (interactions) three variables: source Source node, either metabolite protein interaction Type interaction, 1 = Activation, -1 = Inhibition target Target node, either metabolite protein","code":""},{"path":"/reference/meta_network.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Meta Prior Knowledge Network — meta_network","text":"network available Omnipath:   https://metapkn.omnipathdb.org/metapkn__20200122.txt, scripts    used build network available   https://github.com/saezlab/Meta_PKN.","code":""},{"path":"/reference/meta_network.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Meta Prior Knowledge Network — meta_network","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular    Systems Biology. 17, e9730.","code":""},{"path":"/reference/meta_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Meta Prior Knowledge Network — meta_network","text":"","code":"data(meta_network)"},{"path":"/reference/meta_network_cleanup.html","id":null,"dir":"Reference","previous_headings":"","what":"meta_network_cleanup — meta_network_cleanup","title":"meta_network_cleanup — meta_network_cleanup","text":"function cleans meta network data frame removing self-interactions, calculating mean interaction values duplicated source-target pairs, keeping interactions values 1 -1.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"meta_network_cleanup — meta_network_cleanup","text":"","code":"meta_network_cleanup(meta_network)"},{"path":"/reference/meta_network_cleanup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"meta_network_cleanup — meta_network_cleanup","text":"meta_network data frame columns 'source', 'interaction', 'target'.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"meta_network_cleanup — meta_network_cleanup","text":"cleaned meta network data frame.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"meta_network_cleanup — meta_network_cleanup","text":"","code":"# Create a meta network data frame example_meta_network <- data.frame( source = c(\"A\", \"B\", \"C\", \"D\", \"A\", \"B\", \"C\", \"D\", \"A\"), interaction = c(1, 1, 1, -1, 1, -1, 1, -1, 1), target = c(\"B\", \"C\", \"D\", \"A\", \"C\", \"D\", \"A\", \"B\", \"B\") )  # Clean up the example meta network cleaned_meta_network <- meta_network_cleanup(example_meta_network) #> Warning: `summarise_each()` was deprecated in dplyr 0.7.0. #> ℹ Please use `across()` instead. #> ℹ The deprecated feature was likely used in the cosmosR package. #>   Please report the issue at <https://github.com/saezlab/COSMOSR/issues>. #> Warning: `funs()` was deprecated in dplyr 0.8.0. #> ℹ Please use a list of either functions or lambdas: #>  #> # Simple named list: list(mean = mean, median = median) #>  #> # Auto named with `tibble::lst()`: tibble::lst(mean, median) #>  #> # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) #> ℹ The deprecated feature was likely used in the cosmosR package. #>   Please report the issue at <https://github.com/saezlab/COSMOSR/issues>. print(cleaned_meta_network) #>   source target interaction #> 1      A      B           1 #> 2      A      C           1 #> 3      B      C           1 #> 4      B      D          -1 #> 5      C      A           1 #> 6      C      D           1 #> 7      D      A          -1 #> 8      D      B          -1"},{"path":"/reference/moon.html","id":null,"dir":"Reference","previous_headings":"","what":"moon — moon","title":"moon — moon","text":"Iteratively propagate downstream input activity signed directed network using weighted mean enrichment score decoupleR package","code":""},{"path":"/reference/moon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"moon — moon","text":"","code":"moon(   upstream_input = NULL,   downstream_input,   meta_network,   n_layers,   n_perm = 1000,   downstream_cutoff = 0,   statistic = \"ulm\",   return_levels = F )"},{"path":"/reference/moon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"moon — moon","text":"upstream_input named vector up_stream nodes corresponding activity. downstream_input named vector down_stream nodes corresponding activity. meta_network network data frame containing signed directed prior knowledge molecular interactions. n_layers number layers propagated upstream. n_perm number permutations use decoupleR's algorithm. downstream_cutoff downstream measurments included given threshold statistic decoupleR stat consider: \"wmean\", \"norm_wmean\", \"ulm\" return_levels true false, true layers protein belongs returned alongside scores","code":""},{"path":"/reference/moon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"moon — moon","text":"data frame containing score nodes upstream  downstream input based iterative propagation","code":""},{"path":"/reference/moon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"moon — moon","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"C\", \"D\", \"E\", \"D\", \"B\", \"A\"),   sign = c(1, -1, -1, 1, -1, -1, 1) )  # Run the function with the example input data result <- moon(upstream_input, downstream_input, meta_network, n_layers = 2, statistic = \"wmean\") #> [1] 2  # View the results print(result) #>   source score level #> 1      B  -2.0     1 #> D      D   2.0     0 #> E      E  -1.5     0"},{"path":"/reference/prepare_metab_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"function adds metabolic compartments metabolic identifiers provided user.","code":""},{"path":"/reference/prepare_metab_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"","code":"prepare_metab_inputs(metab_input, compartment_codes)"},{"path":"/reference/prepare_metab_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"metab_input named  vector matebolic statistics inputs metabolite identifiers names compartment_codes character vector, desired compartment codes added. Possible values \"r\", \"c\", \"e\", \"x\", \"m\", \"l\", \"n\" \"g\"","code":""},{"path":"/reference/prepare_metab_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"named vector compartment code prefixed added names","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":null,"dir":"Reference","previous_headings":"","what":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"Runs checks input data simplifies prior knowledge network. Simplification includes removal (1) nodes reachable  signaling nodes  (2) interactions transcription factors target genes target gene respond response contradictory change transcription factor activity.  Optionally, TF activities estimated via network optimization via CARNIVAL interactions TF genes filtered .","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"","code":"preprocess_COSMOS_metabolism_to_signaling(   meta_network = meta_network,   tf_regulon = load_tf_regulon_dorothea(),   signaling_data,   metabolic_data,   diff_expression_data = NULL,   diff_exp_threshold = 1,   maximum_network_depth = 8,   expressed_genes = NULL,   remove_unexpressed_nodes = TRUE,   filter_tf_gene_interaction_by_optimization = TRUE,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"meta_network prior knowledge network (PKN). PKN released COSMOS derived Omnipath, STITCHdb Recon3D can used. See details  data meta_network. tf_regulon collection transcription factor - target interactions. default collection dorothea can obtained  load_tf_regulon_dorothea function. signaling_data numerical vector, names signaling nodes  PKN values {1, 0, -1}. Continuous data  discretized using sign function. metabolic_data numerical vector, names metabolic nodes  PKN values continuous values represents log2 fold change  t-values differential analysis. values compared  simulation results (simulated nodes can take value -1, 0 1) diff_expression_data (optional) numerical vector represents  results differential gene expression analysis. Names gene names using gene symbole values log fold change  t-values. use “diff_exp_threshold” parameter decide  genes changed significantly.  Genes NA values considered none   expressed removed TF-gene expression interactions. diff_exp_threshold threshold parameter (default 1) used binarize values “diff_expression_data”. maximum_network_depth integer > 0 (default: 8). Nodes  “maximum_network_depth” steps signaling nodes directed graph PKN considered non-reachable removed. expressed_genes character vector. Names nodes expressed.  default consider nodes appear diff_expression_data numeric value (.e. nodes NA removed) remove_unexpressed_nodes TRUE (default) removes nodes PKN  expressed, see input “expressed_genes”. filter_tf_gene_interaction_by_optimization (default:TRUE), TRUE runs  network optimization estimates TF activity included inputs checks consistency estimated activity change gene  expression. Removes interactions TF gene expression inconsistent CARNIVAL_options list controls options CARNIVAL. See details  default_CARNIVAL_options.","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"cosmos_data object following fields:  meta_network Filtered PKN tf_regulon TF - target regulatory network signaling_data_bin Binarised signaling data metabolic_data Metabolomics data diff_expression_data_bin Binarized gene expression data optimized_network Initial optimized network      filter_tf_gene_interaction_by_optimization TRUE","code":""},{"path":[]},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_back <- preprocess_COSMOS_metabolism_to_signaling( meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:39 24.06.2024 Carnival flavour: vanilla #> 08:13:39 24.06.2024 Generating variables for lp problem #> 08:13:39 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_39d24_06_2024n47.RData #> 08:13:39 24.06.2024 Generating formulation for LP problem #> 08:13:39 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_39d24_06_2024n47.lp #> 08:13:39 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:39 24.06.2024 Done: solving LP problem. #> 08:13:39 24.06.2024 Getting the solution matrix #> 08:13:39 24.06.2024 Done: getting the solution matrix. #> 08:13:39 24.06.2024 Exporting solution matrix #> 08:13:39 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:39 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":null,"dir":"Reference","previous_headings":"","what":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"Runs checks input data simplifies prior knowledge network. Simplification includes removal (1) nodes reachable  signaling nodes  (2) interactions transcription factors target genes target gene respond response contradictory change transcription factor activity.  Optionally, TF activities estimated via network optimization via CARNIVAL interactions TF genes filtered .","code":""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"","code":"preprocess_COSMOS_signaling_to_metabolism(   meta_network = meta_network,   tf_regulon = load_tf_regulon_dorothea(),   signaling_data,   metabolic_data,   diff_expression_data = NULL,   diff_exp_threshold = 1,   maximum_network_depth = 8,   expressed_genes = NULL,   remove_unexpressed_nodes = TRUE,   filter_tf_gene_interaction_by_optimization = TRUE,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"meta_network prior knowledge network (PKN). PKN released COSMOS derived Omnipath, STITCHdb Recon3D can used. See details  data meta_network. tf_regulon collection transcription factor - target interactions. default collection dorothea can obtained  load_tf_regulon_dorothea function. signaling_data numerical vector, names signaling nodes  PKN values {1, 0, -1}. Continuous data  discretized using sign function. metabolic_data numerical vector, names metabolic nodes  PKN values continuous values represents log2 fold change  t-values differential analysis. values compared  simulation results (simulated nodes can take value -1, 0 1) diff_expression_data (optional) numerical vector represents  results differential gene expression analysis. Names gene names using gene symbole values log fold change  t-values.  use “diff_exp_threshold” parameter decide  genes changed significantly.  Genes NA values considered none  expressed removed TF-gene expression interactions. diff_exp_threshold threshold parameter (default 1) used binarize values “diff_expression_data”. maximum_network_depth integer > 0 (default: 8). Nodes  “maximum_network_depth” steps signaling nodes  directed graph PKN considered non-reachable removed. expressed_genes character vector. Names nodes expressed.  default consider nodes appear diff_expression_data numeric value (.e. nodes NA removed) remove_unexpressed_nodes TRUE (default) removes nodes PKN  expressed, see input “expressed_genes”. filter_tf_gene_interaction_by_optimization (default:TRUE), TRUE runs  network optimization estimates TF activity included inputs checks consistency estimated activity change gene  expression. Removes interactions TF gene expression inconsistent CARNIVAL_options list controls options CARNIVAL. See details  default_CARNIVAL_options.","code":""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"cosmos_data object following fields:  meta_network Filtered PKN tf_regulon TF - target regulatory network signaling_data_bin Binarised signaling data metabolic_data Metabolomics data diff_expression_data_bin Binarized gene expression data optimized_network Initial optimized network      filter_tf_gene_interaction_by_optimization TRUE","code":""},{"path":[]},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,      signaling_data = toy_signaling_input,      metabolic_data = toy_metabolic_input,      diff_expression_data = toy_RNA,      maximum_network_depth = 15,      remove_unexpressed_nodes = TRUE,      CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:39 24.06.2024 Carnival flavour: vanilla #> 08:13:39 24.06.2024 Generating variables for lp problem #> 08:13:39 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_39d24_06_2024n31.RData #> 08:13:39 24.06.2024 Generating formulation for LP problem #> 08:13:39 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_39d24_06_2024n31.lp #> 08:13:39 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:40 24.06.2024 Done: solving LP problem. #> 08:13:40 24.06.2024 Getting the solution matrix #> 08:13:40 24.06.2024 Done: getting the solution matrix. #> 08:13:40 24.06.2024 Exporting solution matrix #> 08:13:40 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:40 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\""},{"path":"/reference/print.cosmos_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"Print Cosmos Data Summary Print summary cosmos data.","code":""},{"path":"/reference/print.cosmos_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"","code":"# S3 method for cosmos_data print(x, ...)"},{"path":"/reference/print.cosmos_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"x cosmos_data object.  Use  preprocess_COSMOS_signaling_to_metabolism  preprocess_COSMOS_metabolism_to_signaling functions  create one. ... print arguments passed methods.","code":""},{"path":"/reference/print.cosmos_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"input (invisible)","code":""},{"path":[]},{"path":"/reference/reduce_solution_network.html","id":null,"dir":"Reference","previous_headings":"","what":"reduce_solution_network — reduce_solution_network","title":"reduce_solution_network — reduce_solution_network","text":"Reduces solution network based decoupling analysis upstream downstream gene expression, filtering edges meet consistency threshold, limiting network certain number steps upstream input nodes.","code":""},{"path":"/reference/reduce_solution_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reduce_solution_network — reduce_solution_network","text":"","code":"reduce_solution_network(   decoupleRnival_res,   meta_network,   cutoff,   upstream_input,   RNA_input = NULL,   n_steps = 10 )"},{"path":"/reference/reduce_solution_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reduce_solution_network — reduce_solution_network","text":"decoupleRnival_res data frame resulting decoupleRnival function. meta_network network data frame containing signed directed prior knowledge molecular interactions. cutoff consistency threshold filtering edges solution network. upstream_input named vector up_stream nodes corresponding activity. RNA_input named vector containing differential gene expression data. n_steps maximum number steps upstream input nodes include solution network.","code":""},{"path":"/reference/reduce_solution_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reduce_solution_network — reduce_solution_network","text":"list containing solution network (SIF) attribute table (ATT) gene expression data.","code":""},{"path":"/reference/reduce_solution_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reduce_solution_network — reduce_solution_network","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"D\", \"D\", \"E\", \"D\", \"B\", \"A\"),   interaction = c(-1, 1, -1, 1, -1, -1, 1) ) RNA_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 5, \"D\" = 0.7, \"E\" = -0.3)  # Run the decoupleRnival function to get the upstream influence scores upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\"  # Reduce the solution network based on the upstream influence scores reduced_network <- reduce_solution_network(upstream_scores, meta_network, 0.4, upstream_input, RNA_input, 3) #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 3 steps\" #> [1] \"COSMOS: 0 from  4 interactions are removed from the PKN\"  # View the resulting solution network and attribute table print(reduced_network$SIF) #>   source target interaction consistency #> 1      A      B          -1        TRUE #> 2      A      D           1        TRUE #> 3      B      D          -1        TRUE #> 6      D      B          -1        TRUE print(reduced_network$ATT) #>   nodes    score RNA_input #> 1     A  1.05659       1.0 #> 2     B -1.05659      -1.0 #> 3     D  2.00000       0.7"},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":null,"dir":"Reference","previous_headings":"","what":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"Runs COSMOS metabolism signaling.  function uses CARNIVAL find subset prior knowledge network based optimization (1)  includes measured input nodes (2) agreement data.  Use preprocess_COSMOS_metabolism_to_signaling  prepare inputs, measurements prior knowledge network.","code":""},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"","code":"run_COSMOS_metabolism_to_signaling(   data,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"data cosmos_data object.  Use  preprocess_COSMOS_metabolism_to_signaling function create  instance. CARNIVAL_options List controls options CARNIVAL. See details  default_CARNIVAL_options.","code":""},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"List following elements:  weightedSIF averaged networks found      optimization format Simple Interaction network, .e. row      codes edge N_networks Number solutions found      optimization nodesAttributes Estimated node properties individual_networks List optimial networks found individual_networks_node_attributes Node activity     network","code":""},{"path":[]},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network,                         signaling_data = toy_signaling_input,                         metabolic_data = toy_metabolic_input,                         diff_expression_data = toy_RNA,                         maximum_network_depth = 15,                         remove_unexpressed_nodes = TRUE,                         CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:41 24.06.2024 Carnival flavour: vanilla #> 08:13:41 24.06.2024 Generating variables for lp problem #> 08:13:41 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n68.RData #> 08:13:41 24.06.2024 Generating formulation for LP problem #> 08:13:41 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n68.lp #> 08:13:41 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:41 24.06.2024 Done: solving LP problem. #> 08:13:41 24.06.2024 Getting the solution matrix #> 08:13:41 24.06.2024 Done: getting the solution matrix. #> 08:13:41 24.06.2024 Exporting solution matrix #> 08:13:41 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:41 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\"  test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back,                        CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:41 24.06.2024 Carnival flavour: vanilla #> 08:13:41 24.06.2024 Generating variables for lp problem #> 08:13:41 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n73.RData #> 08:13:41 24.06.2024 Generating formulation for LP problem #> 08:13:41 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n73.lp #> 08:13:41 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:41 24.06.2024 Done: solving LP problem. #> 08:13:41 24.06.2024 Getting the solution matrix #> 08:13:41 24.06.2024 Done: getting the solution matrix. #> 08:13:41 24.06.2024 Exporting solution matrix #> 08:13:41 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:41 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---"},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":null,"dir":"Reference","previous_headings":"","what":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"Runs COSMOS signaling metabolism.  function uses CARNIVAL find subset prior knowledge network based optimisation (1)  includes measured input nodes (2) agreement data.  Use preprocess_COSMOS_signaling_to_metabolism prepare inputs, measurements prior knowledge network.","code":""},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"","code":"run_COSMOS_signaling_to_metabolism(   data,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"data cosmos_data object.  Use preprocess_COSMOS_signaling_to_metabolism function create instance. CARNIVAL_options List controls options CARNIVAL. See  details default_CARNIVAL_options.","code":""},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"List following elements:  weightedSIF averaged networks found      optimization format Simple Interaction network, .e. row      codes edge N_networks Number solutions found      optimization nodesAttributes Estimated node properties individual_networks List optimial networks found individual_networks_node_attributes Node activity     network","code":""},{"path":[]},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,                              signaling_data = toy_signaling_input,                              metabolic_data = toy_metabolic_input,                              diff_expression_data = toy_RNA,                              maximum_network_depth = 15,                              remove_unexpressed_nodes = TRUE,                              CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:41 24.06.2024 Carnival flavour: vanilla #> 08:13:41 24.06.2024 Generating variables for lp problem #> 08:13:41 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_41d24_06_2024n69.RData #> 08:13:41 24.06.2024 Generating formulation for LP problem #> 08:13:41 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_41d24_06_2024n69.lp #> 08:13:41 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:42 24.06.2024 Done: solving LP problem. #> 08:13:42 24.06.2024 Getting the solution matrix #> 08:13:42 24.06.2024 Done: getting the solution matrix. #> 08:13:42 24.06.2024 Exporting solution matrix #> 08:13:42 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:42 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\"  test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for,                              CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 08:13:42 24.06.2024 Carnival flavour: vanilla #> 08:13:42 24.06.2024 Generating variables for lp problem #> 08:13:42 24.06.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t08_13_42d24_06_2024n5.RData #> 08:13:42 24.06.2024 Generating formulation for LP problem #> 08:13:42 24.06.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t08_13_42d24_06_2024n5.lp #> 08:13:42 24.06.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 08:13:42 24.06.2024 Done: solving LP problem. #> 08:13:42 24.06.2024 Getting the solution matrix #> 08:13:42 24.06.2024 Done: getting the solution matrix. #> 08:13:42 24.06.2024 Exporting solution matrix #> 08:13:42 24.06.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 08:13:42 24.06.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---"},{"path":"/reference/toy_RNA.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Input Transcription Data Set — toy_RNA","title":"Toy Input Transcription Data Set — toy_RNA","text":"exemplary transcription data specific deregulated gene expression 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/toy_RNA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Input Transcription Data Set — toy_RNA","text":"","code":"data(toy_RNA)"},{"path":"/reference/toy_RNA.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Input Transcription Data Set — toy_RNA","text":"object class “numeric” containing t-values   9300 genes, named gene symboles matching toy network.","code":""},{"path":"/reference/toy_RNA.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Input Transcription Data Set — toy_RNA","text":"https://github.com/saezlab/COSMOS_MSB/blob/main/data/RNA_ttop_tumorvshealthy.csv","code":""},{"path":"/reference/toy_RNA.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Toy Input Transcription Data Set — toy_RNA","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular    Systems Biology. 17, e9730.","code":""},{"path":"/reference/toy_RNA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Input Transcription Data Set — toy_RNA","text":"","code":"data(toy_RNA)"},{"path":"/reference/toy_metabolic_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Metabolic Input Data — toy_metabolic_input","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"metabolic data subset metabolic measurements 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/toy_metabolic_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"","code":"data(toy_metabolic_input)"},{"path":"/reference/toy_metabolic_input.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"object class “numeric” containing t-values   2 metabolites, named metabolite HMDB Ids matching   toy network.","code":""},{"path":"/reference/toy_metabolic_input.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"Subset :    https://github.com/saezlab/COSMOS_MSB/blob/main/data/metab_input_COSMOS.csv","code":""},{"path":"/reference/toy_metabolic_input.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular    Systems Biology. 17, e9730.","code":""},{"path":"/reference/toy_metabolic_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Metabolic Input Data — toy_metabolic_input","text":"","code":"data(toy_metabolic_input)"},{"path":"/reference/toy_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Input Network — toy_network","title":"Toy Input Network — toy_network","text":"signaling network reduced COSMOS network solution obtained cosmos test 786-O NCI60 data.  , network solution reused exemplary input prior knowledge network (PKN).","code":""},{"path":"/reference/toy_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Input Network — toy_network","text":"","code":"data(toy_network)"},{"path":"/reference/toy_network.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Input Network — toy_network","text":"object class “data.frame” 19 rows   (interactions) three variables: source Source node, either metabolite protein interaction Type interaction, 1 = Activation, -1 = Inhibition target Target node, either metabolite protein","code":""},{"path":"/reference/toy_network.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Input Network — toy_network","text":"network data available github:   https://github.com/saezlab/COSMOS_MSB/tree/main/results/COSMOS_result/COSMOS_res_session.RData.   toy_network combined network COSMOS network solutions    CARNIVAL_Result2 CARNIVAL_Result_rerun subsequently reduced 19   exemplary nodes.","code":""},{"path":"/reference/toy_network.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Toy Input Network — toy_network","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular    Systems Biology. 17, e9730.","code":""},{"path":"/reference/toy_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Input Network — toy_network","text":"","code":"data(toy_network)"},{"path":"/reference/toy_signaling_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Signaling Input — toy_signaling_input","title":"Toy Signaling Input — toy_signaling_input","text":"signaling data subset footprint-based signaling activity estimates transcription factors 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/toy_signaling_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Signaling Input — toy_signaling_input","text":"","code":"data(toy_signaling_input)"},{"path":"/reference/toy_signaling_input.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Signaling Input — toy_signaling_input","text":"object class “data.frame” containing normalised   enrichment scores (NES) 2 signaling proteins, named   respective gene Entrez ID matching toy network.","code":""},{"path":"/reference/toy_signaling_input.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Signaling Input — toy_signaling_input","text":"Subset :    https://github.com/saezlab/COSMOS_MSB/blob/main/data/signaling_input_COSMOS.csv","code":""},{"path":"/reference/toy_signaling_input.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Toy Signaling Input — toy_signaling_input","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular    Systems Biology. 17, e9730.","code":""},{"path":"/reference/toy_signaling_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Signaling Input — toy_signaling_input","text":"","code":"data(toy_signaling_input)"},{"path":"/reference/translate_column_HMDB.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate Column Using HMDB Mapper — translate_column_HMDB","title":"Translate Column Using HMDB Mapper — translate_column_HMDB","text":"function translates values column using provided Human Metabolome Database (HMDB) mapper vector. modifies input values replacing certain prefixes suffixes according specific rules.","code":""},{"path":"/reference/translate_column_HMDB.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate Column Using HMDB Mapper — translate_column_HMDB","text":"","code":"translate_column_HMDB(my_column, HMDB_mapper_vec)"},{"path":"/reference/translate_column_HMDB.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate Column Using HMDB Mapper — translate_column_HMDB","text":"my_column vector values translated. HMDB_mapper_vec named vector names original identifiers values corresponding HMDB identifiers.","code":""},{"path":"/reference/translate_column_HMDB.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate Column Using HMDB Mapper — translate_column_HMDB","text":"vector translated values.","code":""},{"path":"/reference/translate_column_HMDB.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate Column Using HMDB Mapper — translate_column_HMDB","text":"","code":"# Create a sample column and HMDB mapper vector my_column <- c(\"Metab__1234_a\", \"Gene5678_b\", \"Metab__91011_c\") HMDB_mapper_vec <- c(\"1234\" = \"HMDB00001\", \"5678\" = \"HMDB00002\", \"91011\" = \"HMDB00003\")  # Translate the column translated_column <- translate_column_HMDB(my_column, HMDB_mapper_vec)"},{"path":"/reference/translate_res.html","id":null,"dir":"Reference","previous_headings":"","what":"translate_res — translate_res","title":"translate_res — translate_res","text":"formats network readable names","code":""},{"path":"/reference/translate_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"translate_res — translate_res","text":"","code":"translate_res(SIF, ATT, HMDB_mapper_vec = NULL)"},{"path":"/reference/translate_res.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"translate_res — translate_res","text":"SIF result SIF decoupleRnival pipeline ATT result ATT decoupleRnival pipeline HMDB_mapper_vec named vector HMDB Ids names desired metabolite names values.","code":""},{"path":"/reference/translate_res.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"translate_res — translate_res","text":"list network attribute tables.","code":""},{"path":"/reference/translate_res.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"translate_res — translate_res","text":"","code":"# Create a meta network data frame example_SIF <- data.frame( source = c(\"GPX1\", \"Gene863__GPX1\"), target = c(\"Gene863__GPX1\", \"Metab__HMDB0003337_c\"), sign = c(1, 1) )  example_ATT <- data.frame( Nodes = c(\"GPX1\", \"Gene863__GPX1\",\"Metab__HMDB0003337_c\"), sign = c(1, 1, 1) )  example_SIF #>          source               target sign #> 1          GPX1        Gene863__GPX1    1 #> 2 Gene863__GPX1 Metab__HMDB0003337_c    1  data(\"HMDB_mapper_vec\")  translated_res <- translate_res(example_SIF,example_ATT,HMDB_mapper_vec)  translated_res$SIF #>            source                 target sign #> 1            GPX1        Enzyme863__GPX1    1 #> 2 Enzyme863__GPX1 Metab__Oxiglutatione_c    1"},{"path":"/reference/wide_ulm_res.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert ULM Results to Wide Format — wide_ulm_res","title":"Convert ULM Results to Wide Format — wide_ulm_res","text":"function converts results ULM analysis wide format data frame. input data frame columns source, condition, score. output  data frame row represents source column represents condition, corresponding scores values.","code":""},{"path":"/reference/wide_ulm_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert ULM Results to Wide Format — wide_ulm_res","text":"","code":"wide_ulm_res(ulm_result)"},{"path":"/reference/wide_ulm_res.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert ULM Results to Wide Format — wide_ulm_res","text":"ulm_result data frame representing ULM results columns: source, condition, score.","code":""},{"path":"/reference/wide_ulm_res.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert ULM Results to Wide Format — wide_ulm_res","text":"data frame wide format row source column condition.","code":""},{"path":"/reference/wide_ulm_res.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert ULM Results to Wide Format — wide_ulm_res","text":"","code":"# Create a sample ULM result ulm_result <- data.frame(source = c(\"A\", \"A\", \"B\", \"B\"),                          condition = c(\"cond1\", \"cond2\", \"cond1\", \"cond2\"),                          score = c(0.5, 0.8, 0.3, 0.7))  # Convert to wide format wide_ulm_result <- wide_ulm_res(ulm_result)"},{"path":"/news/index.html","id":"changes-in-version-0992-2020-05-12","dir":"Changelog","previous_headings":"","what":"Changes in version 0.99.2 (2020-05-12)","title":"Changes in version 0.99.2 (2020-05-12)","text":"Submitted bioRxiv Release github page Submitted Bioconductor","code":""}]
+[{"path":"/articles/tutorial.html","id":"installation-and-dependency","dir":"Articles","previous_headings":"","what":"Installation and dependency","title":"COSMOS-tutorial","text":"COSMOS dependent CARNIVAL exhibiting signalling pathway optimisation. CARNIVAL requires interactive version IBM Cplex CBC-COIN solver network optimiser. IBM ILOG Cplex freely available Academic Initiative . CBC solver open source freely available user, significantly lower performance CPLEX. Obtain CBC executable directly usable cosmos . Alternatively small networks, users can rely freely available lpSolve R-package, automatically installed package. tutorial use lpSolve, strongly recommend obtain license CPLEX.","code":"# install from bioconductor if (!requireNamespace(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\") BiocManager::install(\"cosmosR\")   # install the newest (development) version from GitHub # install.packages(\"remotes\") # install CARNIVAL from github  remotes::install_github(\"saezlab/CARNIVAL\") remotes::install_github(\"saezlab/cosmosR\")"},{"path":"/articles/tutorial.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"COSMOS-tutorial","text":"COSMOS (Causal Oriented Search Multi-Omic Space) method integrates phosphoproteomics, transcriptomics, metabolomics data sets. COSMOS leverages extensive prior knowledge signaling pathways, metabolic networks, gene regulation computational methods estimate activities transcription factors kinases well network-level causal reasoning. pipeline can provide mechanistic explanations experimental observations across multiple omic data sets. Essentially, COSMOS 3 main components: prior knowledge: goal COSMOS essentially connect various deregulation events together mechanistic hypotheses. mechanistic hypotheses basically known potential interactions molecular biology features, proteins metabolites. example interaction can activation MTOR AKT, EGFR canonical pathway. Thousands potential interaction can assembled together form large network interactions. networks thus called prior knowledge networks (PKN), summarize large amounts prior knowledge form network. context COSMOS interactions come Omnipath database, STICHdb recon3D reaction network. respect example interaction MTOR AKT, question usually asked presented given experimental context : MTOR can activate AKT general, interaction relevant experimental context? brings us second component COSMOS. data: Information deregulated transcription factors (TF), kinases/phosphophatases metabolites can extracted transcriptomic, phospho-proteomic metabolomic data respectively, using footprint analysis methods (see:https://github.com/saezlab/transcriptutorial (Especially chapter 4)). information can quite useful , characterize TFs kinases specifically deregulated cancer cells example. goal COSMOS find different deregulation events can connected together. Going back example MTOR AKT, know AKT can potentially activate MTOR, observe data AKT MTOR significantly activated cancer tissue compared healthy counterpart, reasonable chance interaction active cancer tissue ’m studying. problem data often contain information hundreds -regulated activities time, thousands potential interactions can potentially explain . order find optimal set interactions relevant explain deregulation observed data, algorithm needed. algorithm: problem described data part formulated integer linear optimisation problem. PKN data can abstracted large set integer variables operating together even larger set equations (see https://www.nature.com/articles/s41540-019-0118-z info). Given set fixed value variable (, subset known deregulation), need find values sets variable (corresponding proteins metabolites information data) can lead satisfying result. satisfying results context COSMOS represent sub-network interactions small possible coherently explaining many known deregulation possible. Thus, set equation mentioned earlier needs solved, using integer linear programming solver. solvers currently available COSMOS lpsolve, cbc cplex. general, CPLEX preferred CBC real case applications, lpsolve mainly used testing small networks sets measurements.","code":""},{"path":"/articles/tutorial.html","id":"tutorial-section-signaling-to-metabolism","dir":"Articles","previous_headings":"","what":"Tutorial section: signaling to metabolism","title":"COSMOS-tutorial","text":"First, load package part, can set options CARNIVAL run, timelimit min gap tolerance. user provide path CPLEX/cbc executable. can check CARNIVAL_options variable see possible options can adjusted example, use built-solver lpSolve. User aware lpSolve used TESTS. obtain meaningful results, best solver cplex, cbc possible. next section, prepare input run cosmosR. signaling inputs result footprint based TF kinase activity estimation. info TF activity estimation transcriptomic data, see:https://github.com/saezlab/transcriptutorial (Especially chapter 4) use toy PKN, see full meta PKN, can load data(meta_network). see meta_PKN assembled, see: https://github.com/saezlab/meta_PKN_BIGG.git metabolites prior knowledge network identified XMetab__HMDBid_compartment XMetab__BIGGid_compartment (example “Metab__HMDB0000190_c”). compartment code BIGG model standard (r, c, e, x, m, l, n, g). Thus first need map whatever identifier metabolite data one network. Genes identified gene symboles (signaling part network) Gene####__symbole (reaction network part network). maximum network depth define maximum number step downstream kinase/TF COSMOS look deregulated metabolites. Good first guess max depth around 4 6 (15 toy dataset) differential experession data used filter wrong TF-target interactions context pre-optimisation. list genes differential expression data also used reference define genes expressed (genes diff_expression_data considered expressed, genes diff_expression_data removed network). , CARNIVAL_options$timelimit set pre-optimisation. Indeed, “filter_tf_gene_interaction_by_optimization” parameter “preprocess_COSMOS_signaling_to_metabolism” function set TRUE, COSMOS can perform first optimisation run order generate preliminary solution network can used filtering incoherences TF activities downstream target expressions. part, can set options actual run, timelimit min gap tolerance. running time much higher pre-optimisation. can increase number threads use many available CPUs. cosmosR run. Finally, process results first cosmosR run, translate gene names metabolites name.","code":"library(cosmosR) CARNIVAL_options <- default_CARNIVAL_options(solver = \"lpSolve\")  # To use CBC # CARNIVAL_options <- default_CARNIVAL_options(solver = \"cbc\") # CARNIVAL_options$solverPath <- \"~/Documents/cbc\" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05  # To use CPLEX: # CARNIVAL_options <- default_CARNIVAL_options(solver = \"cplex\") # CARNIVAL_options$solverPath <- \"C:/Program Files/CPLEX_solver/cplex/bin/x64_win64/cplex.exe\" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05   CARNIVAL_options$timelimit <- 3600 data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,                                         signaling_data = toy_signaling_input,                                         metabolic_data = toy_metabolic_input,                                                       diff_expression_data = toy_RNA,                                                       maximum_network_depth = 15,                                                       remove_unexpressed_nodes = TRUE,                                                       CARNIVAL_options = CARNIVAL_options) ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" ## [1] \"COSMOS: removing unexpressed nodes from PKN...\" ## [1] \"COSMOS: 0 interactions removed\" ## [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" ## [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" ## [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" CARNIVAL_options$timelimit <- 14400 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for,                                                       CARNIVAL_options = CARNIVAL_options) ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" formated_result_for <- format_COSMOS_res(test_result_for)"},{"path":"/articles/tutorial.html","id":"tutorial-section-metabolism-to-signaling","dir":"Articles","previous_headings":"","what":"Tutorial section: metabolism to signaling","title":"COSMOS-tutorial","text":"run metabolism signaling part, need prepare inputs. Now correct time set pre-optimisation run, can prepare inputs. can run cosmosR connect metabolism signaling. running time usually needs longer, problem seems harder solve CPLEX. Finally can format result backward run well (forward run)","code":"CARNIVAL_options$timelimit <- 3600 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network,                                         signaling_data = toy_signaling_input,                                         metabolic_data = toy_metabolic_input,                                                        diff_expression_data = toy_RNA,                                                        maximum_network_depth = 15,                                                        remove_unexpressed_nodes = FALSE,                                                        CARNIVAL_options = CARNIVAL_options) ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" ## [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" ## [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" ## [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" ## [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" ## [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" ## [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" ## [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" ## [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" CARNIVAL_options$timelimit <- 28800  test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back,                                                        CARNIVAL_options = CARNIVAL_options) ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" ## [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" formated_result_back <- format_COSMOS_res(test_result_back)"},{"path":"/articles/tutorial.html","id":"tutorial-section-merge-forward-and-backward-networks-and-visualise-network","dir":"Articles","previous_headings":"","what":"Tutorial section: Merge forward and backward networks and visualise network","title":"COSMOS-tutorial","text":"simply take union forward backward runs create full network solution lopping signaling, gene-regulation metabolism. Since overlap result network forward backward run, may optionally want check node sign incoherent overlap two solutions. function generate dynamic network plot centered given node network solution, connecting measured nodes given range (7 steps). network can intepreted (purely illustrative, interaction may incorectly signed lpsolve can use positive interactions): network represents flow activities can connect MYC -regulation Glucitol (Sorbitol) accumulation. , NFKB1 can upregulate expression SLC2A1, turn transport glucose cytoplasm. increase transport glucose can lead glucose avlaible conversion glucitol AKR1A enzyme. Interestingly, glucitol now activator MAPK14, thus leading appearance positive feedback loop connecting MYC, glucitol MAPK14. important understand links hypothetical. come larger pool potential molecular interactions present multiple online databases compiled omnipath, STITCH recon metabolic network. exist literature interactions known potentially exists experimental contexts. Thus, COSMOS compile potential interactions together proposes coherent set can explain data hand. links however considered potential mechanistic connections, need confirmed experimentally. interactions can searched literature see disease experimental context shown relevant. Taken together, multiple interactions can help build biological story can guide underatanding underlying biology decide future experiments.","code":"full_sif <- as.data.frame(rbind(formated_result_for[[1]], formated_result_back[[1]])) full_sif <- full_sif[full_sif$Weight>0,] full_attributes <- as.data.frame(rbind(formated_result_for[[2]], formated_result_back[[2]]))  full_sif <- unique(full_sif) full_attributes <- unique(full_attributes) network_plot <- display_node_neighboorhood(central_node = 'Metab__D-Glucitol_c',                                             sif = full_sif,                                             att = full_attributes,                                             n = 7)  network_plot"},{"path":"/articles/tutorial.html","id":"tutorial-section-over-representation-analysis","dir":"Articles","previous_headings":"","what":"Tutorial section: Over Representation Analysis","title":"COSMOS-tutorial","text":"Often useful perform Representation Analysis (ORA) resulting nodes COSMOS network first analysis step get functional interpretation modeled signaling cascade. common way test whether selected genes (nodes) COSMOS solution network show statistically significant differences comparison prior-knowledge network (PKN). differentially expressed genes give information cellular processes deregulated proportions various pathways SIGNIFICANTLY different expected.way significant differences two biological conditions (e.g. cancer vs. normal tissue, treatment vs. untreated cells) can shown. Algorithms perform ORA implemented R packages like piano decoupleR. addition gene set collection algorithms require two different lists inputs: - nodes COSMOS solution network relate back input data (e.g. transcriptomics, proteomics, metabolomics, fluxomics, perturbations) - nodes (kinases, transcription factors, metabolites) prior-knowledge network (used background analysis) section show obtain two lists formated COSMOS result object. Now forward backward sets can used ORA analysis.","code":"sif_forward = formated_result_for[[1]] att_forward = formated_result_for[[2]] nodes_ORA = extract_nodes_for_ORA(     sif = sif_forward,      att = att_forward) sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] cosmosR_1.9.1 ##  ## loaded via a namespace (and not attached): ##  [1] bcellViper_1.40.0   sass_0.4.9          utf8_1.2.4          ##  [4] generics_0.1.3      tidyr_1.3.1         lpSolve_5.6.20      ##  [7] stringi_1.8.4       lattice_0.22-6      hms_1.1.3           ## [10] digest_0.6.36       magrittr_2.0.3      evaluate_0.24.0     ## [13] grid_4.4.1          fastmap_1.2.0       jsonlite_1.8.8      ## [16] Matrix_1.7-0        progress_1.2.3      purrr_1.0.2         ## [19] fansi_1.0.6         codetools_0.2-20    textshaping_0.4.0   ## [22] jquerylib_0.1.4     cli_3.6.3           rlang_1.1.4         ## [25] decoupleR_2.10.0    crayon_1.5.3        visNetwork_2.1.2    ## [28] parallelly_1.37.1   bit64_4.0.5         withr_3.0.0         ## [31] cachem_1.1.0        yaml_2.3.9          tools_4.4.1         ## [34] parallel_4.4.1      tzdb_0.4.0          BiocParallel_1.38.0 ## [37] dplyr_1.1.4         vctrs_0.6.5         R6_2.5.1            ## [40] lifecycle_1.0.4     stringr_1.5.1       bit_4.0.5           ## [43] fs_1.6.4            htmlwidgets_1.6.4   vroom_1.6.5         ## [46] ragg_1.3.2          pkgconfig_2.0.3     desc_1.4.3          ## [49] pkgdown_2.1.0       pillar_1.9.0        bslib_0.7.0         ## [52] glue_1.7.0          systemfonts_1.1.0   xfun_0.45           ## [55] tibble_3.2.1        tidyselect_1.2.1    knitr_1.48          ## [58] CARNIVAL_2.14.0     dorothea_1.16.0     rjson_0.2.21        ## [61] igraph_2.0.3        htmltools_0.5.8.1   rmarkdown_2.27      ## [64] readr_2.1.5         compiler_4.4.1      prettyunits_1.2.0"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Aurélien Dugourd. Author. Attila Gabor. Maintainer. Katharina Zirngibl. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B. Emdal, Vitor Vieira, Dorte B. Bekker-Jensen, Jennifer Kranz, Eric. M. J. Bindels, Ana S. H. Costa, Abel sousa, Pedro Beltrao, Jesper V. Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez. 'Causal integration multi-omics data prior knowledge generate mechanistic hypotheses.' Molecular Systems Biology. 2021.","code":"@Article{,   author = {Aurelien Dugourd and Christoph Kuppe and Marco Sciacovelli and Enio Gjerga and Attila Gabor and Kristina B. Embdal and Vitor Vieira and Dorte B. Bekker-Jensen and Jennifer Kranz and Eric M. J. Bindels and Ana S. H. Costa and Abel Sousa and Pedro Beltrao and Jesper V Olsen and Christian Frezza and Rafael Kramann and Julio Saez-Rodriguez},   title = {Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses},   journal = {Molecular Systems Biology},   year = {2021}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"COSMOS (Causal Oriented Search Multi-Omic Space) method integrates phosphoproteomics, transcriptomics, metabolomics data sets. COSMOS leverages extensive prior knowledge signaling pathways, metabolic networks, gene regulation computational methods estimate activities transcription factors kinases well network-level causal reasoning. pipeline can provide mechanistic explanations experimental observations across multiple omic data sets.  COSMOS finds coherent subnetwork causally connecting many deregulated TFs, kinases/phosphatases metabolites possible. subnetwork extracted novel integrated PKN (available ) spanning signaling, transcriptional regulation metabolism. Transcription factors activities inferred gene expression decoupleR. Kinase activities inferred phosphoproteomic kinase/substrate network Omnipath, meta resource protein-protein. scripts generate current network can found : https://github.com/saezlab/meta_PKN_BIGG. can also use COSMOS don’t metabolomic data, connect TF activities (transcriptomic) kinase activities (phosphoproteomic) exmaple !","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"R >= 4.1 required don’t R 4.1, can also clone github repository machine, create new R project R studio cosmosR folder, change R version R version DESCRIPTION file install devtools:install() 4.1 advised case.","code":"# install from bioconductor if (!requireNamespace(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"cosmosR\")  # We advise to instal from github to get the latest version of the tool. if (!requireNamespace(\"devtools\", quietly = TRUE))     install.packages(\"devtools\")      devtools::install_github(\"saezlab/cosmosR\")"},{"path":"/index.html","id":"tutorial-to-use-mofa-nad-cosmos","dir":"","previous_headings":"","what":"tutorial to use MOFA nad COSMOS","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"can find extensive tutorial showing use MOFA COSMOS NCI60 dataset. extensive tutorial, wish get quicker plug play introduction COSMOS, see .","code":""},{"path":"/index.html","id":"tutorial-nci60-playground","dir":"","previous_headings":"","what":"Tutorial (NCI60 playground)","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"made repository contains pre-processed inputs example script use cosmos NCI60 RNA+metabolomic datasets. can find repository .","code":""},{"path":"/index.html","id":"access","dir":"","previous_headings":"","what":"Access","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"meta PKN used biorXiv version COSMOS available . updated meta PKN available package (using data(meta_network) R)","code":""},{"path":"/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"use cosmosR research please cite original publication: Dugourd , Kuppe C, Sciacovelli M, Gjerga E, Gabor , Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Jesper V Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez et al (2021) Causal integration multi-omics data prior knowledge generate mechanistic hypotheses. Mol Syst Biol 17: e9730","code":""},{"path":"/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"COSMOS (Causal Oriented Search of Multi-Omic Space)","text":"code distributed GNU General Public License v3.0. meta PKN distributed Attribution-NonCommercial 4.0 International (CC--NC 4.0) License.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Input Transcription Data Set — HMDB_mapper_vec","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"exemplary transcription data specific deregulated gene expression 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"","code":"data(HMDB_mapper_vec)"},{"path":"/reference/HMDB_mapper_vec.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"object class “character” containing marching HMDB metabolite IDs coresponding metabolite names.","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"https://bioconductor.org/packages/release/data/annotation/html/metaboliteIDmapping.html","code":""},{"path":"/reference/HMDB_mapper_vec.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Toy Input Transcription Data Set — HMDB_mapper_vec","text":"","code":"data(HMDB_mapper_vec)"},{"path":"/reference/compress_same_children.html","id":null,"dir":"Reference","previous_headings":"","what":"Compress Network by Merging Nodes with Identical Children — compress_same_children","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"function compresses network merging nodes children. input network represented data frame three columns: source, target, sign interaction. function returns list containing compressed network, node signatures, duplicated signatures.","code":""},{"path":"/reference/compress_same_children.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"","code":"compress_same_children(df, sig_input, metab_input)"},{"path":"/reference/compress_same_children.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"df data frame representing network three columns: source, target, sign interaction. sig_input list input node signatures considered merging process. metab_input list input metabolic signatures considered merging process.","code":""},{"path":"/reference/compress_same_children.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"list containing following elements: compressed_network data frame representing compressed network. node_signatures list signatures nodes network merging process. duplicated_signatures list duplicated signatures network merging process.","code":""},{"path":"/reference/compress_same_children.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compress Network by Merging Nodes with Identical Children — compress_same_children","text":"","code":"# Create a sample network df <- data.frame(source = c(\"A\", \"A\", \"B\", \"B\"),                  target = c(\"C\", \"D\", \"C\", \"D\"),                  sign_of_interaction = c(1, 1, 1, 1))  # Define input node and metabolic signatures sig_input <- list() metab_input <- list()  # Compress the network result <- compress_same_children(df, sig_input, metab_input) compressed_network <- result$compressed_network"},{"path":"/reference/cosmos_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Cosmos Data — cosmos_data","title":"Create Cosmos Data — cosmos_data","text":"S3 class combines required data comprehensive list.  Use preprocess_COSMOS_signaling_to_metabolism preprocess_COSMOS_metabolism_to_signaling create instance.","code":""},{"path":"/reference/cosmos_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Cosmos Data — cosmos_data","text":"","code":"cosmos_data(   meta_network,   tf_regulon = NULL,   signaling_data,   metabolic_data,   expression_data,   verbose = TRUE )"},{"path":"/reference/cosmos_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Cosmos Data — cosmos_data","text":"meta_network Prior knowledge network (PKN).  default COSMOS use PKN derived Omnipath, STITCHdb Recon3D.  See details data meta_network. tf_regulon Collection transcription factor - target interactions. default collection dorothea can obtained load_tf_regulon_dorothea function. signaling_data Numerical vector, names signaling nodes PKN values {1, 0, -1}.  Continuous data discretized using sign function. metabolic_data Numerical vector, names metabolic nodes PKN values continuous values represents log2 fold change t-values differential analysis.  values compared simulation results (simulated nodes can take value -1, 0 1). expression_data Numerical vector represents results differential gene expression analysis. Names gene names using EntrezID starting X values log fold change t-values. Genes NA values considered none expressed removed TF-gene expression interactions. verbose (default: TRUE) Reports details cosmos_data object.","code":""},{"path":"/reference/cosmos_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Cosmos Data — cosmos_data","text":"cosmos data class instance.","code":""},{"path":"/reference/createLinearColors.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Linear Colors Based on Numeric Input — createLinearColors","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"function generates gradient colors based provided numeric values. colors can adjusted include zero configurable specified maximum custom color palette.","code":""},{"path":"/reference/createLinearColors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"","code":"createLinearColors(   numbers,   withZero = T,   maximum = 100,   my_colors = c(\"royalblue3\", \"white\", \"red\") )"},{"path":"/reference/createLinearColors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"numbers numeric vector color gradient generated. withZero logical value indicating whether zero included color gradient. Default TRUE. maximum integer specifying maximum number colors generated gradient. Default 100. my_colors character vector length three specifying colors used gradient. Default c(\"royalblue3\", \"white\", \"red\").","code":""},{"path":"/reference/createLinearColors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"character vector colors representing gradient based input numeric values.","code":""},{"path":"/reference/createLinearColors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Linear Colors Based on Numeric Input — createLinearColors","text":"","code":"# Generate colors for a set of numbers including zero numbers <- c(-50, -20, 0, 20, 50) colors <- createLinearColors(numbers, withZero = TRUE, maximum = 100)"},{"path":"/reference/decompress_moon_result.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompress Moon Result — decompress_moon_result","title":"Decompress Moon Result — decompress_moon_result","text":"function decompresses results obtained moon analysis incorporating node signatures handling duplicated parents. merges details provided meta network data returns comprehensive data frame.","code":""},{"path":"/reference/decompress_moon_result.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompress Moon Result — decompress_moon_result","text":"","code":"decompress_moon_result(moon_res, meta_network_compressed_list, meta_network)"},{"path":"/reference/decompress_moon_result.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompress Moon Result — decompress_moon_result","text":"moon_res data frame containing results moon analysis. meta_network_compressed_list list containing compressed meta network details, including node signatures duplicated parents. meta_network data frame representing original meta network.","code":""},{"path":"/reference/decompress_moon_result.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompress Moon Result — decompress_moon_result","text":"data frame merges moon analysis results meta network data,         including additional details node signatures handling duplicated parents.","code":""},{"path":"/reference/decompress_moon_result.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompress Moon Result — decompress_moon_result","text":"","code":"# Example usage (requires appropriate data structures for moon_res,  # meta_network_compressed_list, and meta_network) # decompressed_result <- decompress_moon_result(moon_res, meta_network_compressed_list, meta_network)"},{"path":"/reference/decompress_solution_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompress Solution Network — decompress_solution_network","title":"Decompress Solution Network — decompress_solution_network","text":"function decompresses solution network mapping node signatures back original identifiers. input formatted solution network, meta network, node signatures, duplicated parents. function returns list containing decompressed solution network attribute table.","code":""},{"path":"/reference/decompress_solution_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompress Solution Network — decompress_solution_network","text":"","code":"decompress_solution_network(   formatted_res,   meta_network,   node_signatures,   duplicated_parents )"},{"path":"/reference/decompress_solution_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompress Solution Network — decompress_solution_network","text":"formatted_res list containing solution network attribute table. meta_network data frame representing meta network. node_signatures list node signatures. duplicated_parents list duplicated parents compression process.","code":""},{"path":"/reference/decompress_solution_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompress Solution Network — decompress_solution_network","text":"list containing following elements: SIF data frame representing decompressed solution network. ATT data frame containing attributes decompressed solution network.","code":""},{"path":"/reference/decompress_solution_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompress Solution Network — decompress_solution_network","text":"","code":"# Create a sample formatted_res formatted_res <- list(   SIF = data.frame(source = c(\"parent_of_D1\", \"D\"),                    target = c(\"D\", \"F\"),                    interaction = c(1, 1),                    Weight = c(1, 1)),   ATT = data.frame(Nodes = c(\"parent_of_D1\", \"D\", \"F\"),                    NodeType = c(\"\",\"\",\"\"),                    ZeroAct = c(0,0,0),                    UpAct = c(1,1,1),                    DownAct = c(0,0,0),                    AvgAct = c(1,1,1),                    measured = c(0,0,0),                    Activity = c(1,1,1)) )  # Create a sample meta_network meta_network <- data.frame(source = c(\"A\", \"B\", \"D\"),                            target = c(\"D\", \"D\", \"F\"),                            interaction_type = c(1, 1, 1))  # Define node_signatures and duplicated_parents node_signatures <- list(\"A\" = \"parent_of_D1\",\"B\" = \"parent_of_D1\",\"D\" = \"parent_F1\") duplicated_parents <- c(\"A\" = \"parent_of_D1\",\"B\" = \"parent_of_D1\")  # Decompress the solution network result <- decompress_solution_network(formatted_res, meta_network, node_signatures, duplicated_parents) decompressed_network <- result[[1]] attribute_table <- result[[2]]"},{"path":"/reference/decoupleRnival.html","id":null,"dir":"Reference","previous_headings":"","what":"DecoupleRnival — decoupleRnival","title":"DecoupleRnival — decoupleRnival","text":"Iteratively propagate downstream input activity signed directed network using weighted mean enrichment score decoupleR package","code":""},{"path":"/reference/decoupleRnival.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DecoupleRnival — decoupleRnival","text":"","code":"decoupleRnival(   upstream_input = NULL,   downstream_input,   meta_network,   n_layers,   n_perm = 1000,   downstream_cutoff = 0,   statistic = \"norm_wmean\" )"},{"path":"/reference/decoupleRnival.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DecoupleRnival — decoupleRnival","text":"upstream_input named vector up_stream nodes corresponding activity. downstream_input named vector down_stream nodes corresponding activity. meta_network network data frame containing signed directed prior knowledge molecular interactions. n_layers number layers propagated upstream. n_perm number permutations use decoupleR's algorithm. downstream_cutoff downstream measurments included given threshold statistic decoupleR stat consider: \"wmean\", \"norm_wmean\", \"ulm\"","code":""},{"path":"/reference/decoupleRnival.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DecoupleRnival — decoupleRnival","text":"data frame containing score nodes upstream downstream input based iterative propagation","code":""},{"path":"/reference/decoupleRnival.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DecoupleRnival — decoupleRnival","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"C\", \"D\", \"E\", \"D\", \"B\", \"A\"),   sign = c(1, -1, -1, 1, -1, -1, 1) )  # Run the function with the example input data result <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\" #> [1] 2  # View the results print(result) #>   source    score #> 1      B -1.05659 #> D      D  2.00000 #> E      E -1.50000"},{"path":"/reference/default_CARNIVAL_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Setting Default CARNIVAL Options — default_CARNIVAL_options","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"Returns default CARNIVAL options list.  can modify elements list use argument run_COSMOS_metabolism_to_signaling  run_COSMOS_signaling_to_metabolism. choose CPLEX CBC, must modify solverPath field point CPLEX/CBC executable (See Details).","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"","code":"default_CARNIVAL_options(solver = NULL)"},{"path":"/reference/default_CARNIVAL_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"solver one `cplex` (recommended, require 3rd party tool), `cbc` (also require 3rd party tool) `lpSolve` (small networks)","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"returns list possible options implemented CARNIVAL. see documentation runCARNIVAL.","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"COSMOS dependent CARNIVAL exhibiting signalling pathway optimisation. CARNIVAL requires interactive version IBM Cplex, Gurobi CBC-COIN solver  network optimiser. IBM ILOG Cplex freely available Academic Initiative . Gurobi license also free academics, request license following instructions .  CBC solver open source freely available user, significantly lower performance CPLEX Gurobi. Obtain CBC executable directly usable cosmos . Alternatively small networks, users can rely freely available  lpSolve R-package,  automatically installed package.","code":""},{"path":"/reference/default_CARNIVAL_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Setting Default CARNIVAL Options — default_CARNIVAL_options","text":"","code":"# load and change default options:  my_options = default_CARNIVAL_options(solver = \"cplex\")   my_options$solverPath = \"/Applications/CPLEX_Studio128/cplex/bin/x86-64_osx/cplex\" my_options$threads = 2 my_options$timelimit = 3600*15"},{"path":"/reference/display_node_neighboorhood.html","id":null,"dir":"Reference","previous_headings":"","what":"display_node_neighboorhood — display_node_neighboorhood","title":"display_node_neighboorhood — display_node_neighboorhood","text":"display input measurements within n steps given set nodes","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"display_node_neighboorhood — display_node_neighboorhood","text":"","code":"display_node_neighboorhood(central_node, sif, att, n = 100)"},{"path":"/reference/display_node_neighboorhood.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"display_node_neighboorhood — display_node_neighboorhood","text":"central_node character character vector; node ID(s) around network branched untill meansurments input reached sif df; COSMOS network solution sif format like first list element returned format_cosmos_res function att df; attributes nodes COMSOS network solution like second list element returned format_cosmos_res function n numeric; maximum number steps network look inputs measurments","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"display_node_neighboorhood — display_node_neighboorhood","text":"visnetwork object","code":""},{"path":"/reference/display_node_neighboorhood.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"display_node_neighboorhood — display_node_neighboorhood","text":"","code":"CARNIVAL_options <- cosmosR::default_CARNIVAL_options(\"lpSolve\") data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:30 15.07.2024 Carnival flavour: vanilla #> 09:38:30 15.07.2024 Generating variables for lp problem #> 09:38:30 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_30d15_07_2024n45.RData #> 09:38:30 15.07.2024 Generating formulation for LP problem #> 09:38:30 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_30d15_07_2024n45.lp #> 09:38:30 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:31 15.07.2024 Done: solving LP problem. #> 09:38:31 15.07.2024 Getting the solution matrix #> 09:38:31 15.07.2024 Done: getting the solution matrix. #> 09:38:31 15.07.2024 Exporting solution matrix #> 09:38:31 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:31 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:31 15.07.2024 Carnival flavour: vanilla #> 09:38:31 15.07.2024 Generating variables for lp problem #> 09:38:31 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_31d15_07_2024n23.RData #> 09:38:31 15.07.2024 Generating formulation for LP problem #> 09:38:31 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_31d15_07_2024n23.lp #> 09:38:31 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:31 15.07.2024 Done: solving LP problem. #> 09:38:31 15.07.2024 Getting the solution matrix #> 09:38:31 15.07.2024 Done: getting the solution matrix. #> 09:38:31 15.07.2024 Exporting solution matrix #> 09:38:31 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:31 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  test_result_for <- format_COSMOS_res(test_result_for) network_plot <- display_node_neighboorhood(central_node = 'MYC', sif = test_result_for[[1]], att = test_result_for[[2]], n = 7) #> Warning: At vendor/cigraph/src/paths/unweighted.c:444 : Couldn't reach some vertices. network_plot  {\"x\":{\"nodes\":{\"id\":[\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"FGFR1\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucitol_c\",\"Metab__D-Glucose_c\",\"Metab__L-Lactic acid_c\",\"SLC2A1\"],\"NodeType\":[\"\",\"\",\"\",\"\",\"\",\"\",\"P\",\"M\",\"\",\"M\",\"\"],\"ZeroAct\":[0,0,0,0,0,0,0,0,0,0,0],\"UpAct\":[1,1,1,1,1,1,1,1,1,1,1],\"DownAct\":[0,0,0,0,0,0,0,0,0,0,0],\"AvgAct\":[1,1,1,1,1,1,1,1,1,1,1],\"measured\":[0,0,0,0,0,0,1,1,0,1,0],\"Activity\":[1,1,1,1,1,1,1,1,1,1,1],\"label\":[\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"FGFR1\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucitol_c\",\"Metab__D-Glucose_c\",\"Metab__L-Lactic acid_c\",\"SLC2A1\"],\"color\":[\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\",\"green\"],\"shape\":[\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\",\"dot\"],\"shadow\":[false,false,false,false,false,false,true,true,false,true,false]},\"edges\":{\"from\":[\"MAPK14\",\"Metab__D-Glucitol_c\",\"FGFR1\",\"Enzyme1338__AKR1A1\",\"Enzyme7338__LDHB_LDHA_reverse\",\"Enzyme9049__SLC2A1_reverse\",\"LDHA\",\"MAPK14\",\"MYC\",\"Metab__D-Glucose_c\",\"SLC2A1\"],\"to\":[\"MYC\",\"MAPK14\",\"LDHA\",\"Metab__D-Glucitol_c\",\"Metab__L-Lactic acid_c\",\"Metab__D-Glucose_c\",\"Enzyme7338__LDHB_LDHA_reverse\",\"FGFR1\",\"SLC2A1\",\"Enzyme1338__AKR1A1\",\"Enzyme9049__SLC2A1_reverse\"],\"sign\":[1,1,1,1,1,1,1,-1,1,1,1],\"weigth\":[1,1,1,1,1,1,1,0,1,1,1],\"color\":[\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\",\"grey\"],\"arrows.to.type\":[\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"arrow\",\"circle\",\"arrow\",\"arrow\",\"arrow\"],\"enabled\":[true,true,true,true,true,true,true,true,true,true,true],\"scaleFactor\":[1,1,1,1,1,1,1,1,1,1,1]},\"nodesToDataframe\":true,\"edgesToDataframe\":true,\"options\":{\"width\":\"100%\",\"height\":\"100%\",\"nodes\":{\"shape\":\"dot\"},\"manipulation\":{\"enabled\":false}},\"groups\":null,\"width\":1600,\"height\":1600,\"idselection\":{\"enabled\":true,\"style\":\"width: 200px; height: 26px;\\n                                              background: #f8f8f8;\\n                                              color: darkblue;\\n                                              border:none;\\n                                              outline:none;\",\"useLabels\":true,\"main\":\"Select by id\"},\"byselection\":{\"enabled\":false,\"style\":\"width: 150px; height: 26px\",\"multiple\":false,\"hideColor\":\"rgba(200,200,200,0.5)\",\"highlight\":false},\"main\":null,\"submain\":null,\"footer\":null,\"background\":\"rgba(0, 0, 0, 0)\",\"highlight\":{\"enabled\":true,\"hoverNearest\":false,\"degree\":1,\"algorithm\":\"all\",\"hideColor\":\"rgba(200,200,200,0.5)\",\"labelOnly\":true},\"collapse\":{\"enabled\":false,\"fit\":false,\"resetHighlight\":true,\"clusterOptions\":null,\"keepCoord\":true,\"labelSuffix\":\"(cluster)\"}},\"evals\":[],\"jsHooks\":[]}"},{"path":"/reference/extract_nodes_for_ORA.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"Function extract nodes appear COSMOS output network background genes (genes present prior knowledge network)","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"","code":"extract_nodes_for_ORA(sif, att)"},{"path":"/reference/extract_nodes_for_ORA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"sif df; COSMOS network solution sif format like first list element returned format_cosmos_res function att df; attributes nodes COMSOS network solution like second list element returned format_cosmos_res function","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"List 2 objects: success background genes","code":""},{"path":"/reference/extract_nodes_for_ORA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract COSMOS nodes for ORA analysis — extract_nodes_for_ORA","text":"","code":"CARNIVAL_options <- cosmosR::default_CARNIVAL_options(\"lpSolve\") data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:32 15.07.2024 Carnival flavour: vanilla #> 09:38:32 15.07.2024 Generating variables for lp problem #> 09:38:32 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_32d15_07_2024n76.RData #> 09:38:32 15.07.2024 Generating formulation for LP problem #> 09:38:32 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_32d15_07_2024n76.lp #> 09:38:32 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:32 15.07.2024 Done: solving LP problem. #> 09:38:32 15.07.2024 Getting the solution matrix #> 09:38:32 15.07.2024 Done: getting the solution matrix. #> 09:38:32 15.07.2024 Exporting solution matrix #> 09:38:32 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:32 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:32 15.07.2024 Carnival flavour: vanilla #> 09:38:32 15.07.2024 Generating variables for lp problem #> 09:38:32 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_32d15_07_2024n63.RData #> 09:38:32 15.07.2024 Generating formulation for LP problem #> 09:38:32 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_32d15_07_2024n63.lp #> 09:38:32 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:33 15.07.2024 Done: solving LP problem. #> 09:38:33 15.07.2024 Getting the solution matrix #> 09:38:33 15.07.2024 Done: getting the solution matrix. #> 09:38:33 15.07.2024 Exporting solution matrix #> 09:38:33 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:33 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  test_result_for <- format_COSMOS_res(test_result_for) extreacted_nodes <- extract_nodes_for_ORA( sif = test_result_for[[1]], att = test_result_for[[2]] )"},{"path":"/reference/filter_incohrent_TF_target.html","id":null,"dir":"Reference","previous_headings":"","what":"filter_incohrent_TF_target — filter_incohrent_TF_target","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"Filters incoherent target genes regulatory network based decoupling analysis upstream downstream gene expression.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"","code":"filter_incohrent_TF_target(   decouplRnival_res,   TF_reg_net,   meta_network,   RNA_input )"},{"path":"/reference/filter_incohrent_TF_target.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"decouplRnival_res data frame resulting decoupleRnival function. TF_reg_net data frame containing prior knowledge transcription factor (TF) regulatory interactions. meta_network network data frame containing signed directed prior knowledge molecular interactions. RNA_input named vector containing differential gene expression data.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"network data frame containing genes incoherently regulated TFs.","code":""},{"path":"/reference/filter_incohrent_TF_target.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"filter_incohrent_TF_target — filter_incohrent_TF_target","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"D\", \"D\", \"E\", \"D\", \"B\", \"A\"),   interaction = c(-1, 1, -1, 1, -1, -1, 1) ) RNA_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 5, \"D\" = -0.7, \"E\" = -0.3)  TF_reg_net <- data.frame( source = c(\"B\"), target = c(\"D\"), mor = c(-1) )  # Run the decoupleRnival function to get the upstream influence scores upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\"  filtered_network <- filter_incohrent_TF_target(upstream_scores, TF_reg_net, meta_network, RNA_input)  print(filtered_network) #>   source target interaction #> 1      A      B          -1 #> 2      A      D           1 #> 4      C      E           1 #> 5      C      D          -1 #> 6      D      B          -1 #> 7      E      A           1"},{"path":"/reference/format_COSMOS_res.html","id":null,"dir":"Reference","previous_headings":"","what":"format_COSMOS_res — format_COSMOS_res","title":"format_COSMOS_res — format_COSMOS_res","text":"formats network readable names","code":""},{"path":"/reference/format_COSMOS_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"format_COSMOS_res — format_COSMOS_res","text":"","code":"format_COSMOS_res(cosmos_res, metab_mapping = NULL)"},{"path":"/reference/format_COSMOS_res.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"format_COSMOS_res — format_COSMOS_res","text":"cosmos_res results COSMOS run metab_mapping named vector HMDB Ids names desired metabolite names values.","code":""},{"path":"/reference/format_COSMOS_res.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"format_COSMOS_res — format_COSMOS_res","text":"list network attribute tables.","code":""},{"path":"/reference/format_LR_ressource.html","id":null,"dir":"Reference","previous_headings":"","what":"Format Ligand-Receptor Resource — format_LR_ressource","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"function formats ligand-receptor resource creating gene set source-target pairs, converting long format, adding default values 'mor' 'likelihood'.","code":""},{"path":"/reference/format_LR_ressource.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"","code":"format_LR_ressource(ligrec_ressource)"},{"path":"/reference/format_LR_ressource.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"ligrec_ressource data frame representing ligand-receptor resource columns source target gene symbols.","code":""},{"path":"/reference/format_LR_ressource.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"data frame containing formatted ligand-receptor gene set columns: gene gene symbol ligand-receptor pairs. set set identifier combining source target gene symbols. mor Default value set 1 entries. likelihood Default value set 1 entries.","code":""},{"path":"/reference/format_LR_ressource.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format Ligand-Receptor Resource — format_LR_ressource","text":"","code":"# Create a sample ligand-receptor resource ligrec_ressource <- data.frame(source_genesymbol = c(\"L1\", \"L2\"),                                target_genesymbol = c(\"R1\", \"R2\"))  # Format the ligand-receptor resource formatted_geneset <- format_LR_ressource(ligrec_ressource)"},{"path":"/reference/get_moon_scoring_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Moon Scoring Network — get_moon_scoring_network","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"function analyzes given meta network based moon scores upstream node. filters processes network controlling observing neighbours according specified parameters. function returns list containing filtered network updated moon scores.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"","code":"get_moon_scoring_network(   upstream_node,   meta_network,   moon_scores,   keep_upstream_node_peers = F )"},{"path":"/reference/get_moon_scoring_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"upstream_node node network analysis starts. meta_network complete network data. moon_scores Scores associated node network. keep_upstream_node_peers Logical; whether keep peers upstream node. Default FALSE.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"list two elements:   - `SIF`: data frame representing filtered meta network.   - `ATT`: data frame representing updated moon scores.","code":""},{"path":"/reference/get_moon_scoring_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Moon Scoring Network — get_moon_scoring_network","text":"","code":"# Example usage (requires appropriate data structures for meta_network and moon_scores) # result <- get_moon_scoring_network(upstream_node, meta_network, moon_scores)"},{"path":"/reference/gmt_to_dataframe.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert gmt file to data frame — gmt_to_dataframe","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"function designed convert gmt file (gene set file MSigDB) two column data frame first column corresponds omic features (genes) second column associated terms (pathway gene belongs ). One gene can belong several pathways.","code":""},{"path":"/reference/gmt_to_dataframe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"","code":"gmt_to_dataframe(gmtfile)"},{"path":"/reference/gmt_to_dataframe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"gmtfile full path name gmt file converted","code":""},{"path":"/reference/gmt_to_dataframe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert gmt file to data frame — gmt_to_dataframe","text":"two column data frame first column corresponds omic features second column associated terms (pathways).","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":null,"dir":"Reference","previous_headings":"","what":"load transcription factor regulon — load_tf_regulon_dorothea","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"load transcription factors DOROTHEA package converts gene symbols EntrezID using org.Hs.eg.db","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"","code":"load_tf_regulon_dorothea(confidence = c(\"A\", \"B\", \"C\"))"},{"path":"/reference/load_tf_regulon_dorothea.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"confidence strong vector (default: c(\"\",\"B\",\"C\")). Subset {, B,  C, D, E}. See `dorothea` meaning confidence levels. package details.","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"returns PKN form data table. row interaction. Columns names : - `tf` transcription factor - `confidence` class confidence - `target` target gene - `sign` indicates interaction (1) -regulation (-1).","code":""},{"path":"/reference/load_tf_regulon_dorothea.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"load transcription factor regulon — load_tf_regulon_dorothea","text":"","code":"load_tf_regulon_dorothea() #> # A tibble: 13,223 × 3 #>    tf    target    sign #>    <chr> <chr>    <dbl> #>  1 AHR   CYP1A1       1 #>  2 AHR   CYP1A2       1 #>  3 AHR   CYP1B1       1 #>  4 AHR   FOS          1 #>  5 AHR   MYC          1 #>  6 AHR   UGT1A6       1 #>  7 AHR   ASAP1        1 #>  8 AHR   ERG          1 #>  9 AHR   VGLL4        1 #> 10 AHR   ARHGAP15     1 #> # ℹ 13,213 more rows"},{"path":"/reference/make_heatmap_color_palette.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Heatmap Color Palette — make_heatmap_color_palette","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"function generates color palette suitable heatmaps based values matrix. uses `createLinearColors` function generate separate color gradients positive negative values.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"","code":"make_heatmap_color_palette(my_matrix)"},{"path":"/reference/make_heatmap_color_palette.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"my_matrix numeric matrix heatmap color palette generated.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"character vector colors representing heatmap color palette based input matrix values.","code":""},{"path":"/reference/make_heatmap_color_palette.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Heatmap Color Palette — make_heatmap_color_palette","text":"","code":"# Create a sample matrix my_matrix <- matrix(c(-3, -1, 0, 1, 3), nrow = 1)  # Generate heatmap color palette heatmap_palette <- make_heatmap_color_palette(my_matrix)"},{"path":"/reference/meta_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Meta Prior Knowledge Network — meta_network","title":"Meta Prior Knowledge Network — meta_network","text":"Comprehensive Prior Knowledge Network (PKN), combines signaling metabolic interaction networks.  network constructed using Recon3D STITCH metabolic networks well signaling network OmniPath.","code":""},{"path":"/reference/meta_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Meta Prior Knowledge Network — meta_network","text":"","code":"data(meta_network)"},{"path":"/reference/meta_network.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Meta Prior Knowledge Network — meta_network","text":"object class “tibble” 117065 rows   (interactions) three variables: source Source node, either metabolite protein interaction Type interaction, 1 = Activation, -1 = Inhibition target Target node, either metabolite protein","code":""},{"path":"/reference/meta_network.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Meta Prior Knowledge Network — meta_network","text":"network available Omnipath:   https://metapkn.omnipathdb.org/metapkn__20200122.txt, scripts   used build network available   https://github.com/saezlab/Meta_PKN.","code":""},{"path":"/reference/meta_network.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Meta Prior Knowledge Network — meta_network","text":"Dugourd, ., Kuppe, C. Sciacovelli, M. et. al. (2021) Molecular   Systems Biology. 17, e9730.","code":""},{"path":"/reference/meta_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Meta Prior Knowledge Network — meta_network","text":"","code":"data(meta_network)"},{"path":"/reference/meta_network_cleanup.html","id":null,"dir":"Reference","previous_headings":"","what":"meta_network_cleanup — meta_network_cleanup","title":"meta_network_cleanup — meta_network_cleanup","text":"function cleans meta network data frame removing self-interactions, calculating mean interaction values duplicated source-target pairs, keeping interactions values 1 -1.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"meta_network_cleanup — meta_network_cleanup","text":"","code":"meta_network_cleanup(meta_network)"},{"path":"/reference/meta_network_cleanup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"meta_network_cleanup — meta_network_cleanup","text":"meta_network data frame columns 'source', 'interaction', 'target'.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"meta_network_cleanup — meta_network_cleanup","text":"cleaned meta network data frame.","code":""},{"path":"/reference/meta_network_cleanup.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"meta_network_cleanup — meta_network_cleanup","text":"","code":"# Create a meta network data frame example_meta_network <- data.frame( source = c(\"A\", \"B\", \"C\", \"D\", \"A\", \"B\", \"C\", \"D\", \"A\"), interaction = c(1, 1, 1, -1, 1, -1, 1, -1, 1), target = c(\"B\", \"C\", \"D\", \"A\", \"C\", \"D\", \"A\", \"B\", \"B\") )  # Clean up the example meta network cleaned_meta_network <- meta_network_cleanup(example_meta_network) #> Warning: `summarise_each()` was deprecated in dplyr 0.7.0. #> ℹ Please use `across()` instead. #> ℹ The deprecated feature was likely used in the cosmosR package. #>   Please report the issue at <https://github.com/saezlab/COSMOSR/issues>. #> Warning: `funs()` was deprecated in dplyr 0.8.0. #> ℹ Please use a list of either functions or lambdas: #>  #> # Simple named list: list(mean = mean, median = median) #>  #> # Auto named with `tibble::lst()`: tibble::lst(mean, median) #>  #> # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) #> ℹ The deprecated feature was likely used in the cosmosR package. #>   Please report the issue at <https://github.com/saezlab/COSMOSR/issues>. print(cleaned_meta_network) #>   source target interaction #> 1      A      B           1 #> 2      A      C           1 #> 3      B      C           1 #> 4      B      D          -1 #> 5      C      A           1 #> 6      C      D           1 #> 7      D      A          -1 #> 8      D      B          -1"},{"path":"/reference/moon.html","id":null,"dir":"Reference","previous_headings":"","what":"moon — moon","title":"moon — moon","text":"Iteratively propagate downstream input activity signed directed network using weighted mean enrichment score decoupleR package","code":""},{"path":"/reference/moon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"moon — moon","text":"","code":"moon(   upstream_input = NULL,   downstream_input,   meta_network,   n_layers,   n_perm = 1000,   downstream_cutoff = 0,   statistic = \"ulm\",   return_levels = F )"},{"path":"/reference/moon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"moon — moon","text":"upstream_input named vector up_stream nodes corresponding activity. downstream_input named vector down_stream nodes corresponding activity. meta_network network data frame containing signed directed prior knowledge molecular interactions. n_layers number layers propagated upstream. n_perm number permutations use decoupleR's algorithm. downstream_cutoff downstream measurments included given threshold statistic decoupleR stat consider: \"wmean\", \"norm_wmean\", \"ulm\" return_levels true false, true layers protein belongs returned alongside scores","code":""},{"path":"/reference/moon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"moon — moon","text":"data frame containing score nodes upstream downstream input based iterative propagation","code":""},{"path":"/reference/moon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"moon — moon","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"C\", \"D\", \"E\", \"D\", \"B\", \"A\"),   sign = c(1, -1, -1, 1, -1, -1, 1) )  # Run the function with the example input data result <- moon(upstream_input, downstream_input, meta_network, n_layers = 2, statistic = \"wmean\") #> [1] 2  # View the results print(result) #>   source score level #> 1      B  -2.0     1 #> D      D   2.0     0 #> E      E  -1.5     0"},{"path":"/reference/prepare_metab_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"function adds metabolic compartments metabolic identifiers provided user.","code":""},{"path":"/reference/prepare_metab_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"","code":"prepare_metab_inputs(metab_input, compartment_codes)"},{"path":"/reference/prepare_metab_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"metab_input named  vector matebolic statistics inputs metabolite identifiers names compartment_codes character vector, desired compartment codes added. Possible values \"r\", \"c\", \"e\", \"x\", \"m\", \"l\", \"n\" \"g\"","code":""},{"path":"/reference/prepare_metab_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"add metabolic compartment and metab__ prefix to metabolite IDs — prepare_metab_inputs","text":"named vector compartment code prefixed added names","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":null,"dir":"Reference","previous_headings":"","what":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"Runs checks input data simplifies prior knowledge network. Simplification includes removal (1) nodes reachable signaling nodes  (2) interactions transcription factors target genes target gene respond response contradictory change transcription factor activity. Optionally, TF activities estimated via network optimization via CARNIVAL interactions TF genes filtered .","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"","code":"preprocess_COSMOS_metabolism_to_signaling(   meta_network = meta_network,   tf_regulon = load_tf_regulon_dorothea(),   signaling_data,   metabolic_data,   diff_expression_data = NULL,   diff_exp_threshold = 1,   maximum_network_depth = 8,   expressed_genes = NULL,   remove_unexpressed_nodes = TRUE,   filter_tf_gene_interaction_by_optimization = TRUE,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"meta_network prior knowledge network (PKN). PKN released COSMOS derived Omnipath, STITCHdb Recon3D can used. See details data meta_network. tf_regulon collection transcription factor - target interactions. default collection dorothea can obtained load_tf_regulon_dorothea function. signaling_data numerical vector, names signaling nodes PKN values {1, 0, -1}. Continuous data discretized using sign function. metabolic_data numerical vector, names metabolic nodes PKN values continuous values represents log2 fold change t-values differential analysis. values compared simulation results (simulated nodes can take value -1, 0 1) diff_expression_data (optional) numerical vector represents results differential gene expression analysis. Names gene names using gene symbole values log fold change  t-values. use “diff_exp_threshold” parameter decide  genes changed significantly.  Genes NA values considered none  expressed removed TF-gene expression interactions. diff_exp_threshold threshold parameter (default 1) used binarize values “diff_expression_data”. maximum_network_depth integer > 0 (default: 8). Nodes “maximum_network_depth” steps signaling nodes directed graph PKN considered non-reachable removed. expressed_genes character vector. Names nodes expressed. default consider nodes appear diff_expression_data numeric value (.e. nodes NA removed) remove_unexpressed_nodes TRUE (default) removes nodes PKN expressed, see input “expressed_genes”. filter_tf_gene_interaction_by_optimization (default:TRUE), TRUE runs network optimization estimates TF activity included inputs checks consistency estimated activity change gene expression. Removes interactions TF gene expression inconsistent CARNIVAL_options list controls options CARNIVAL. See details default_CARNIVAL_options.","code":""},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"cosmos_data object following fields: meta_network Filtered PKN tf_regulon TF - target regulatory network signaling_data_bin Binarised signaling data metabolic_data Metabolomics data diff_expression_data_bin Binarized gene expression data optimized_network Initial optimized network     filter_tf_gene_interaction_by_optimization TRUE","code":""},{"path":[]},{"path":"/reference/preprocess_COSMOS_metabolism_to_signaling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preprocess COSMOS Inputs For Metabolism to Signaling — preprocess_COSMOS_metabolism_to_signaling","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_back <- preprocess_COSMOS_metabolism_to_signaling( meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") ) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:36 15.07.2024 Carnival flavour: vanilla #> 09:38:36 15.07.2024 Generating variables for lp problem #> 09:38:36 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_36d15_07_2024n47.RData #> 09:38:36 15.07.2024 Generating formulation for LP problem #> 09:38:36 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_36d15_07_2024n47.lp #> 09:38:36 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:36 15.07.2024 Done: solving LP problem. #> 09:38:36 15.07.2024 Getting the solution matrix #> 09:38:36 15.07.2024 Done: getting the solution matrix. #> 09:38:36 15.07.2024 Exporting solution matrix #> 09:38:37 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:37 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":null,"dir":"Reference","previous_headings":"","what":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"Runs checks input data simplifies prior knowledge network. Simplification includes removal (1) nodes reachable signaling nodes  (2) interactions transcription factors target genes target gene respond response contradictory change transcription factor activity. Optionally, TF activities estimated via network optimization via CARNIVAL interactions TF genes filtered .","code":""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"","code":"preprocess_COSMOS_signaling_to_metabolism(   meta_network = meta_network,   tf_regulon = load_tf_regulon_dorothea(),   signaling_data,   metabolic_data,   diff_expression_data = NULL,   diff_exp_threshold = 1,   maximum_network_depth = 8,   expressed_genes = NULL,   remove_unexpressed_nodes = TRUE,   filter_tf_gene_interaction_by_optimization = TRUE,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"meta_network prior knowledge network (PKN). PKN released COSMOS derived Omnipath, STITCHdb Recon3D can used. See details data meta_network. tf_regulon collection transcription factor - target interactions. default collection dorothea can obtained load_tf_regulon_dorothea function. signaling_data numerical vector, names signaling nodes PKN values {1, 0, -1}. Continuous data discretized using sign function. metabolic_data numerical vector, names metabolic nodes PKN values continuous values represents log2 fold change t-values differential analysis. values compared simulation results (simulated nodes can take value -1, 0 1) diff_expression_data (optional) numerical vector represents results differential gene expression analysis. Names gene names using gene symbole values log fold change  t-values.  use “diff_exp_threshold” parameter decide  genes changed significantly.  Genes NA values considered none  expressed removed TF-gene expression interactions. diff_exp_threshold threshold parameter (default 1) used binarize values “diff_expression_data”. maximum_network_depth integer > 0 (default: 8). Nodes “maximum_network_depth” steps signaling nodes directed graph PKN considered non-reachable removed. expressed_genes character vector. Names nodes expressed. default consider nodes appear diff_expression_data numeric value (.e. nodes NA removed) remove_unexpressed_nodes TRUE (default) removes nodes PKN expressed, see input “expressed_genes”. filter_tf_gene_interaction_by_optimization (default:TRUE), TRUE runs network optimization estimates TF activity included inputs checks consistency estimated activity change gene expression. Removes interactions TF gene expression inconsistent CARNIVAL_options list controls options CARNIVAL. See details default_CARNIVAL_options.","code":""},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"cosmos_data object following fields: meta_network Filtered PKN tf_regulon TF - target regulatory network signaling_data_bin Binarised signaling data metabolic_data Metabolomics data diff_expression_data_bin Binarized gene expression data optimized_network Initial optimized network     filter_tf_gene_interaction_by_optimization TRUE","code":""},{"path":[]},{"path":"/reference/preprocess_COSMOS_signaling_to_metabolism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preprocess COSMOS Inputs For Signaling to Metabolism — preprocess_COSMOS_signaling_to_metabolism","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,      signaling_data = toy_signaling_input,      metabolic_data = toy_metabolic_input,      diff_expression_data = toy_RNA,      maximum_network_depth = 15,      remove_unexpressed_nodes = TRUE,      CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:37 15.07.2024 Carnival flavour: vanilla #> 09:38:37 15.07.2024 Generating variables for lp problem #> 09:38:37 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_37d15_07_2024n31.RData #> 09:38:37 15.07.2024 Generating formulation for LP problem #> 09:38:37 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_37d15_07_2024n31.lp #> 09:38:37 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:37 15.07.2024 Done: solving LP problem. #> 09:38:37 15.07.2024 Getting the solution matrix #> 09:38:37 15.07.2024 Done: getting the solution matrix. #> 09:38:37 15.07.2024 Exporting solution matrix #> 09:38:37 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:37 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\""},{"path":"/reference/print.cosmos_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"Print Cosmos Data Summary Print summary cosmos data.","code":""},{"path":"/reference/print.cosmos_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"","code":"# S3 method for class 'cosmos_data' print(x, ...)"},{"path":"/reference/print.cosmos_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"x cosmos_data object.  Use preprocess_COSMOS_signaling_to_metabolism preprocess_COSMOS_metabolism_to_signaling functions create one. ... print arguments passed methods.","code":""},{"path":"/reference/print.cosmos_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print Cosmos Data Summary Print a summary of cosmos data. — print.cosmos_data","text":"input (invisible)","code":""},{"path":[]},{"path":"/reference/reduce_solution_network.html","id":null,"dir":"Reference","previous_headings":"","what":"reduce_solution_network — reduce_solution_network","title":"reduce_solution_network — reduce_solution_network","text":"Reduces solution network based decoupling analysis upstream downstream gene expression, filtering edges meet consistency threshold, limiting network certain number steps upstream input nodes.","code":""},{"path":"/reference/reduce_solution_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reduce_solution_network — reduce_solution_network","text":"","code":"reduce_solution_network(   decoupleRnival_res,   meta_network,   cutoff,   upstream_input,   RNA_input = NULL,   n_steps = 10 )"},{"path":"/reference/reduce_solution_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reduce_solution_network — reduce_solution_network","text":"decoupleRnival_res data frame resulting decoupleRnival function. meta_network network data frame containing signed directed prior knowledge molecular interactions. cutoff consistency threshold filtering edges solution network. upstream_input named vector up_stream nodes corresponding activity. RNA_input named vector containing differential gene expression data. n_steps maximum number steps upstream input nodes include solution network.","code":""},{"path":"/reference/reduce_solution_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reduce_solution_network — reduce_solution_network","text":"list containing solution network (SIF) attribute table (ATT) gene expression data.","code":""},{"path":"/reference/reduce_solution_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reduce_solution_network — reduce_solution_network","text":"","code":"# Example input data upstream_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 0.5) downstream_input <- c(\"D\" = 2, \"E\" = -1.5) meta_network <- data.frame(   source = c(\"A\", \"A\", \"B\", \"C\", \"C\", \"D\", \"E\"),   target = c(\"B\", \"D\", \"D\", \"E\", \"D\", \"B\", \"A\"),   interaction = c(-1, 1, -1, 1, -1, -1, 1) ) RNA_input <- c(\"A\" = 1, \"B\" = -1, \"C\" = 5, \"D\" = 0.7, \"E\" = -0.3)  # Run the decoupleRnival function to get the upstream influence scores upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100) #> [1] \"Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead\"  # Reduce the solution network based on the upstream influence scores reduced_network <- reduce_solution_network(upstream_scores, meta_network, 0.4, upstream_input, RNA_input, 3) #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 3 steps\" #> [1] \"COSMOS: 0 from  4 interactions are removed from the PKN\"  # View the resulting solution network and attribute table print(reduced_network$SIF) #>   source target interaction consistency #> 1      A      B          -1        TRUE #> 2      A      D           1        TRUE #> 3      B      D          -1        TRUE #> 6      D      B          -1        TRUE print(reduced_network$ATT) #>   nodes    score RNA_input #> 1     A  1.05659       1.0 #> 2     B -1.05659      -1.0 #> 3     D  2.00000       0.7"},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":null,"dir":"Reference","previous_headings":"","what":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"Runs COSMOS metabolism signaling.  function uses CARNIVAL find subset prior knowledge network based optimization (1) includes measured input nodes (2) agreement data.  Use preprocess_COSMOS_metabolism_to_signaling prepare inputs, measurements prior knowledge network.","code":""},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"","code":"run_COSMOS_metabolism_to_signaling(   data,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"data cosmos_data object.  Use preprocess_COSMOS_metabolism_to_signaling function create instance. CARNIVAL_options List controls options CARNIVAL. See details default_CARNIVAL_options.","code":""},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"List following elements: weightedSIF averaged networks found     optimization format Simple Interaction network, .e. row     codes edge N_networks Number solutions found     optimization nodesAttributes Estimated node properties individual_networks List optimial networks found individual_networks_node_attributes Node activity     network","code":""},{"path":[]},{"path":"/reference/run_COSMOS_metabolism_to_signaling.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"run COSMOS metabolism to signaling — run_COSMOS_metabolism_to_signaling","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network,                         signaling_data = toy_signaling_input,                         metabolic_data = toy_metabolic_input,                         diff_expression_data = toy_RNA,                         maximum_network_depth = 15,                         remove_unexpressed_nodes = TRUE,                         CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 54 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 1 input/measured nodes are not in PKN any more: Metab__HMDB0000190_c and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:39 15.07.2024 Carnival flavour: vanilla #> 09:38:39 15.07.2024 Generating variables for lp problem #> 09:38:39 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n68.RData #> 09:38:39 15.07.2024 Generating formulation for LP problem #> 09:38:39 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n68.lp #> 09:38:39 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:39 15.07.2024 Done: solving LP problem. #> 09:38:39 15.07.2024 Getting the solution matrix #> 09:38:39 15.07.2024 Done: getting the solution matrix. #> 09:38:39 15.07.2024 Exporting solution matrix #> 09:38:39 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:39 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 1 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\"  test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back,                        CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:39 15.07.2024 Carnival flavour: vanilla #> 09:38:39 15.07.2024 Generating variables for lp problem #> 09:38:39 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n73.RData #> 09:38:39 15.07.2024 Generating formulation for LP problem #> 09:38:39 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n73.lp #> 09:38:39 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 842 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:39 15.07.2024 Done: solving LP problem. #> 09:38:39 15.07.2024 Getting the solution matrix #> 09:38:39 15.07.2024 Done: getting the solution matrix. #> 09:38:39 15.07.2024 Exporting solution matrix #> 09:38:39 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:39 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---"},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":null,"dir":"Reference","previous_headings":"","what":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"Runs COSMOS signaling metabolism.  function uses CARNIVAL find subset prior knowledge network based optimisation (1) includes measured input nodes (2) agreement data.  Use preprocess_COSMOS_signaling_to_metabolism prepare inputs, measurements prior knowledge network.","code":""},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"","code":"run_COSMOS_signaling_to_metabolism(   data,   CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\") )"},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"data cosmos_data object.  Use preprocess_COSMOS_signaling_to_metabolism function create instance. CARNIVAL_options List controls options CARNIVAL. See details default_CARNIVAL_options.","code":""},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"List following elements: weightedSIF averaged networks found     optimization format Simple Interaction network, .e. row     codes edge N_networks Number solutions found     optimization nodesAttributes Estimated node properties individual_networks List optimial networks found individual_networks_node_attributes Node activity     network","code":""},{"path":[]},{"path":"/reference/run_COSMOS_signaling_to_metabolism.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"run COSMOS signaling to metabolism — run_COSMOS_signaling_to_metabolism","text":"","code":"data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network,                              signaling_data = toy_signaling_input,                              metabolic_data = toy_metabolic_input,                              diff_expression_data = toy_RNA,                              maximum_network_depth = 15,                              remove_unexpressed_nodes = TRUE,                              CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"COSMOS: all 3 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\" #> [1] \"COSMOS: removing unexpressed nodes from PKN...\" #> [1] \"COSMOS: 0 interactions removed\" #> [1] \"COSMOS: removing nodes that are not reachable from inputs within 15 steps\" #> [1] \"COSMOS: 0 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: removing nodes that are not observable by measurements within 15 steps\" #> [1] \"COSMOS: 52 from  101 interactions are removed from the PKN\" #> [1] \"COSMOS: 2 input/measured nodes are not in PKN any more: USF1, SRF and 0 more.\" #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:39 15.07.2024 Carnival flavour: vanilla #> 09:38:39 15.07.2024 Generating variables for lp problem #> 09:38:39 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_39d15_07_2024n69.RData #> 09:38:39 15.07.2024 Generating formulation for LP problem #> 09:38:39 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_39d15_07_2024n69.lp #> 09:38:39 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:40 15.07.2024 Done: solving LP problem. #> 09:38:40 15.07.2024 Getting the solution matrix #> 09:38:40 15.07.2024 Done: getting the solution matrix. #> 09:38:40 15.07.2024 Exporting solution matrix #> 09:38:40 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:40 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---  #> [1] \"COSMOS:  0 interactions are removed from the PKN based on consistency check between TF activity and gene expression\" #> [1] \"COSMOS: all 1 signaling nodes from data were found in the meta PKN\" #> [1] \"COSMOS: all 2 metabolic nodes from data were found in the meta PKN\" #> [1] \"COSMOS: 2975 of the 9300 genes in expression data were found as transcription factor target\" #> [1] \"COSMOS: 2975 of the 5321 transcription factor targets were found in expression data\"  test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for,                              CARNIVAL_options = default_CARNIVAL_options(\"lpSolve\")) #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> Input nodes should have values from {-1, 0, 1}. We discretize your input with sign(). #> [1] \"lpSolve does not scale well with large PKNs. This solver is mainly for testing purposes. To run COSMSO, we recommend using cplex, or cbc solvers.\" #> --- Start of the CARNIVAL pipeline --- #> 09:38:40 15.07.2024 Carnival flavour: vanilla #> 09:38:40 15.07.2024 Generating variables for lp problem #> 09:38:40 15.07.2024 Done: generating variables for lp problem #> Saving preprocessed data. #> Done: saving parsed data: /__w/cosmosR/cosmosR/docs/reference//parsedData_t09_38_40d15_07_2024n5.RData #> 09:38:40 15.07.2024 Generating formulation for LP problem #> 09:38:40 15.07.2024 Done: generating formulation for LP problem. #> Saving LP file #> Done: Saving LP file: /__w/cosmosR/cosmosR/docs/reference//lpFile_t09_38_40d15_07_2024n5.lp #> 09:38:40 15.07.2024 Solving LP problem #> Parsing .lp file for lpSolve #> Rows: 882 Columns: 1 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (1): X1 #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> Done: parsing .lp file for lpSolve #> 09:38:40 15.07.2024 Done: solving LP problem. #> 09:38:40 15.07.2024 Getting the solution matrix #> 09:38:40 15.07.2024 Done: getting the solution matrix. #> 09:38:40 15.07.2024 Exporting solution matrix #> 09:38:40 15.07.2024 Done: exporting solution matrix. #> Cleaning intermediate files #> Done: cleaning #> 09:38:40 15.07.2024 All tasks finished. #>  #> --- End of the CARNIVAL pipeline ---"},{"path":"/reference/toy_RNA.html","id":null,"dir":"Reference","previous_headings":"","what":"Toy Input Transcription Data Set — toy_RNA","title":"Toy Input Transcription Data Set — toy_RNA","text":"exemplary transcription data specific deregulated gene expression 786-O cell line NCI60 dataset.","code":""},{"path":"/reference/toy_RNA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Toy Input Transcription Data Set — toy_RNA","text":"","code":"data(toy_RNA)"},{"path":"/reference/toy_RNA.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Toy Input Transcription Data Set — toy_RNA","text":"object class “numeric” containing t-values   9300 genes, named gene symboles matching toy network.","code":""},{"path":"/reference/toy_RNA.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Toy Input Transcription Data Set — toy_RNA","text":"https://github.com/saezlab/COSMOS_MSB/blob/main/data/RNA_ttop_tumorvshealthy.csv","code":""},{"path":"/reference/toy_RNA.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Toy Input Transcription Data Set — toy_RNA","text":"Dugourd, ., Kuppe, C. 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+