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<KODAMA >
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>KODAMA</title>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css">
<style>
/* Navbar Styles */
.navbar {
background-color: #333;
border-radius: 10px;
}
.navbar-nav .nav-link {
color: white;
transition: color 0.3s;
}
.navbar-nav .nav-link:hover {
color: #007bff;
}
.navbar-brand {
color: white;
font-size: 24px;
}
/* Section Styles */
section {
margin-top: 20px;
padding: 20px;
border-radius: 10px;
background-color: #f9f9f9;
box-shadow: 0px 0px 20px rgba(0, 0, 0, 0.1);
}
section h1 {
color: #007bff;
margin-bottom: 20px;
}
/* Card Styles */
.card {
border: none;
border-radius: 10px;
box-shadow: 0 4px 8px rgba(0,0,0,0.1);
transition: transform 0.3s;
cursor: pointer;
}
.card:hover {
transform: translateY(-5px);
}
.card-body {
text-align: center;
}
/* Code Styles */
pre {
background-color: #f8f9fa;
border: 1px solid #dee2e6;
border-radius: 5px;
padding: 10px;
overflow-x: auto;
position: relative;
cursor: pointer;
}
pre:hover::after {
content: "";
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100%;
background-color: rgba(0, 0, 255, 0.1); /* Blue color when hovered */
border-radius: 5px;
z-index: 1;
}
pre:hover::before {
content: "\f0ea"; /* FontAwesome copy icon */
font-family: "Font Awesome 5 Free";
position: absolute;
top: 50%;
left: 50%;
transform: translate(-50%, -50%);
font-size: 20px;
color: #007bff;
z-index: 2;
}
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border: 1px solid #dee2e6;
border-radius: 5px;
padding: 10px;
background-color: #f8f9fa;
margin-top: 20px;
cursor: pointer;
display: inline-block;
position: relative;
}
.copy-box:hover {
background-color: #e9ecef;
}
.copy-box::before {
content: "\f0c5"; /* FontAwesome copy icon */
font-family: "Font Awesome 5 Free";
position: absolute;
top: 50%;
left: 5px;
transform: translateY(-50%);
font-size: 18px;
color: #007bff;
}
</style>
</head>
<body>
<!-- Navbar -->
<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
<div class="container">
<a class="navbar-brand" href="#">KODAMA</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarSupportedContent">
<ul class="navbar-nav mr-auto">
<li class="nav-item">
<a class="nav-link" href="#introduction">Introduction</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#software-tutorial">Software Tutorial</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#simulation">Simulation</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Data Analyses
</a>
<div class="dropdown-menu" aria-labelledby="navbarDropdown">
<a class="dropdown-item" href="https://github.com/tkcaccia/KODAMA/blob/main/docs/Metabolomics_data.md">Metabolomic data</a>
<a class="dropdown-item" href="https://github.com/tkcaccia/KODAMA/blob/main/docs/Single_cell_RNA_seq.md">Single cell RNA seq data</a>
<a class="dropdown-item" href="https://github.com/tkcaccia/KODAMA/blob/main/docs/Spatial%20_transcriptomic.md">Spatial Transcriptomic data</a>
</div>
</li>
</ul>
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link" href="https://github.com/tkcaccia/KODAMA">
<span class="fab fa-github"></span>
Source code
</a>
</li>
</ul>
</div>
</div>
</nav>
<!-- Introduction Section -->
<section id="introduction">
<div class="container">
<h1>Introduction</h1>
<p>
# KODAMA An unsupervised and semi-supervised learning algorithm to perform feature extraction from noisy and high-dimensional data
</p>
</div>
</section>
<!-- News Section -->
<section>
<div class="container">
<h2>News</h2>
<p>
<span style="color: black;">KODAMA facilitates identification of patterns representing underlying groups on all samples in a data set.
This is an improved version of KODAMA algorithm for spatially-aware dimensionality reduction. A landmarks procedure has been implemented to adapt the algorithm to the analysis of data set with more than 10,000 entries.</span>
</p>
<p>
<span style="color: black;">The KODAMA package has been integrated with t-SNE and UMAP to convert the KODAMA's dissimilarity matrix in a low dimensional space.</span>
</p>
<p>
<ul>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9887019/" style="color: blue; text-decoration: underline;">Zinga, M. M., Abdel-Shafy, E., Melak, T., Vignoli, A., Piazza, S., Zerbini, L. F., ... & Cacciatore, S. (2022). KODAMA exploratory analysis in metabolic phenotyping. Frontiers in Molecular Biosciences, 9.</a></li>
<li><a href="https://academic.oup.com/bioinformatics/article/33/4/621/2667156?login=false" style="color: blue; text-decoration: underline;">Cacciatore, S., Tenori, L., Luchinat, C., Bennett, P. R., & MacIntyre, D. A. (2017). KODAMA: an R package for knowledge discovery and data mining. Bioinformatics, 33(4), 621-623.</a></li>
<li><a href="https://www.pnas.org/doi/abs/10.1073/pnas.1220873111" style="color: blue; text-decoration: underline;">Cacciatore, S., Luchinat, C., & Tenori, L. (2014). Knowledge discovery by accuracy maximization. Proceedings of the National Academy of Sciences, 111(14), 5117-5122.</a></li>
</ul>
</p>
</div>
</section>
<!-- Installation Section -->
<section>
<div class="container">
<h2>Installation</h2>
<p>
The KODAMA is available on <a href="https://CRAN.R-project.org/package=KODAMA">CRAN</a>.
</p>
<pre><code>library(devtools)
install_github("tkcaccia/KODAMA")
</code></pre>
</div>
</section>
<!-- Applications Section -->
<section>
<div class="container">
<h2>Applications</h2>
<div class="card-deck">
<div class="card">
<div class="card-body">
<h5 class="card-title">Metabolomic data</h5>
<p class="card-text">Explore Metabolomic data</p>
</div>
</div>
<div class="card">
<div class="card-body">
<h5 class="card-title">Single cell RNA seq data</h5>
<p class="card-text">Explore Single cell RNA seq data</p>
</div>
</div>
<div class="card">
<div class="card-body">
<h5 class="card-title">Spatial Transcriptomic data</h5>
<p class="card-text">Explore Spatial Transcriptomic data</p>
</div>
</div>
</div>
</div>
</section>
<!-- Bootstrap Scripts -->
<script src="https://code.jquery.com/jquery-3.5.1.slim.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/@popperjs/core@2.5.3/dist/umd/popper.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js"></script>
<!-- Copy R Code Script -->
<script>
document.getElementById('r-code').addEventListener('click', function() {
var rCode = this.textContent.trim();
var temp = document.createElement('textarea');
temp.value = rCode;
document.body.appendChild(temp);
temp.select();
document.execCommand('copy');
document.body.removeChild(temp);
alert('R code copied to clipboard!');
});
</script>
</body>
</html>