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ZhenyiWangTHU · Sep 27, 2024 · 9ac9b7f · 9ac9b7f
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diff --git a/.Rproj.user/F5A33326/sources/session-32279071/lock_file b/.Rproj.user/F5A33326/sources/session-32279071/lock_file
diff --git a/_book/index.html b/_book/index.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-09-25" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -264,7 +264,7 @@ <h1>
 <div id="header">
 <h1 class="title">HemaScope Tutorial</h1>
 <p class="author"><em>HemaScope team</em></p>
-<p class="date"><em>2024-09-25</em></p>
+<p class="date"><em>2024-09-27</em></p>
 </div>
 <div id="introduction" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">1</span> Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/_book/installation.html b/_book/installation.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-09-25" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/_book/integrated-scrna-seq-pipeline.html b/_book/integrated-scrna-seq-pipeline.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-09-25" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/_book/search_index.json b/_book/search_index.json
diff --git a/_book/step-by-step-scrna-seq-pipeline.html b/_book/step-by-step-scrna-seq-pipeline.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-09-25" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/_book/stey-by-step-st-seq-pipeline.html b/_book/stey-by-step-st-seq-pipeline.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-09-25" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />

diff --git a/docs/index.html b/docs/index.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-07-20" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -56,7 +56,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -264,7 +264,7 @@ <h1>
 <div id="header">
 <h1 class="title">HemaScope Tutorial</h1>
 <p class="author"><em>HemaScope team</em></p>
-<p class="date"><em>2024-07-20</em></p>
+<p class="date"><em>2024-09-27</em></p>
 </div>
 <div id="introduction" class="section level1 hasAnchor" number="1">
 <h1><span class="header-section-number">1</span> Introduction<a href="index.html#introduction" class="anchor-section" aria-label="Anchor link to header"></a></h1>

diff --git a/docs/installation.html b/docs/installation.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-07-20" />
+<meta name="date" content="2024-09-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -56,7 +56,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -294,10 +294,10 @@ <h2><span class="header-section-number">2.2</span> Set the channels in conda<a h
 <div id="install-r-and-python" class="section level2 hasAnchor" number="2.3">
 <h2><span class="header-section-number">2.3</span> Install R and python<a href="installation.html#install-r-and-python" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <ul>
-<li>R 4.3.3 and python 3.11.4</li>
+<li>R 4.3.3 and python 3.8.19</li>
 </ul>
 <pre><code>conda install R-base=4.3.3
-conda install python=3.11.4</code></pre>
+conda install python=3.8.19</code></pre>
 </div>
 <div id="install-required-r-packages" class="section level2 hasAnchor" number="2.4">
 <h2><span class="header-section-number">2.4</span> Install required R-packages<a href="installation.html#install-required-r-packages" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -340,13 +340,17 @@ <h2><span class="header-section-number">2.4</span> Install required R-packages<a
 <li>From CRAN</li>
 </ul>
 <pre><code>remotes::install_version(&quot;shinyjs&quot;, version = &quot;2.1.0&quot;)
+remotes::install_version(&quot;shiny&quot;, version = &quot;1.8.0&quot;)
+remotes::install_version(&quot;shinyWidgets&quot;, version = &quot;0.8.6&quot;)
+remotes::install_version(&quot;shinydashboard&quot;, version = &quot;0.7.2&quot;)
+remotes::install_version(&quot;slickR&quot;, version = &quot;0.6.0&quot;)
 remotes::install_version(&quot;phateR&quot;, version = &quot;1.0.7&quot;)
 remotes::install_version(&quot;gelnet&quot;, version = &quot;1.2.1&quot;)
 remotes::install_version(&quot;parallelDist&quot;, version = &quot;0.2.6&quot;)
 remotes::install_version(&quot;kableExtra&quot;, version = &quot;1.3.4&quot;)
 remotes::install_version(&quot;transport&quot;, version = &quot;0.14-6&quot;)
 remotes::install_version(&quot;feather&quot;, version = &quot;0.3.5&quot;)
-remotes::install_version(&quot;markdown&quot;, version = &quot;1.10&quot;)</code></pre>
+remotes::install_version(&quot;markdown&quot;, version = &quot;1.13&quot;)</code></pre>
 <ul>
 <li>From GitHub</li>
 </ul>
@@ -381,7 +385,7 @@ <h2><span class="header-section-number">2.5</span> Install required Python-packa
 <ul>
 <li>Install required packages</li>
 </ul>
-<pre><code>pip install anndata==0.10.8 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.9.1 networkx==3.3 numpy==1.26.4 pandas==2.0.3 phate==1.0.11 pot==0.9.4 scanpy==1.10.2 scipy==1.13.1 scvelo==0.3.2 scvi-tools==1.1.5 seaborn==0.13.2</code></pre>
+<pre><code>pip install stereopy==1.3.1 anndata==0.9.2 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.7.1 networkx==3.1 numpy==1.23.5 pandas==1.5.3 phate==1.0.11 pot==0.9.1 scanpy==1.9.6 scipy==1.10.1 scvelo==0.3.2 scvi-tools==0.20.3 seaborn==0.12.2</code></pre>
 </div>
 <div id="the-installed-packages-with-versions" class="section level2 hasAnchor" number="2.6">
 <h2><span class="header-section-number">2.6</span> The installed packages with versions<a href="installation.html#the-installed-packages-with-versions" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -608,7 +612,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 magrittr    2.0.3
 maps    3.4.2
 maptools    1.1-8
-markdown    1.1
+markdown    1.13
 MASS    7.3-60.0.1
 Matrix  1.6-5
 MatrixGenerics  1.12.2
@@ -751,8 +755,11 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 SeuratWrappers  0.3.1
 shadowtext  0.1.4
 shape   1.4.6.1
-shiny   1.8.1.1
 shinyjs 2.1.0
+shiny 1.8.0
+shinyWidgets 0.8.6
+shinydashboard 0.7.2
+slickR 0.6.0
 SingleCellExperiment    1.22.0
 sitmo   2.0.2
 slam    0.1-51