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ZhenyiWangTHU · Oct 25, 2024 · a77d87e · a77d87e
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diff --git a/.Rproj.user/F5A33326/bookdown-crossref/01-HemaScope_installation_tutorial.Rmd.xref b/.Rproj.user/F5A33326/bookdown-crossref/01-HemaScope_installation_tutorial.Rmd.xref
@@ -3,6 +3,5 @@ h2:create-a-new-conda-environment-and-activate-it Create a new conda environment
 h2:set-the-channels-in-conda Set the channels in conda
 h2:install-r Install R
 h2:install-required-r-packages Install required R-packages
-h2:create-the-required-python-v.3.9.12-virtual-environment Create the required python (v.3.9.12) virtual environment
-h2:the-installed-packages-with-versions The installed packages with versions
+h2:create-the-required-python-virtual-environment Create the required python virtual environment
 
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diff --git a/.Rproj.user/F5A33326/sources/per/t/9679D688-contents b/.Rproj.user/F5A33326/sources/per/t/9679D688-contents
@@ -34,10 +34,6 @@ conda config --set show_channel_urls true
 
 ## Install R
 
-<<<<<<< Updated upstream
-<!-- - R 4.3.3 and python 3.9.12 -->
-=======
->>>>>>> Stashed changes
 - R 4.3.3
 
 ```
@@ -164,7 +160,7 @@ devtools::install_github(repo="ZhenyiWangTHU/HemaScopeR", dep = FALSE)
 <!-- # stereopy==1.3.1 -->
 <!-- ``` -->
 
-## Create the required python (v.3.9.12) virtual environment
+## Create the required python virtual environment
 
 -   Run the `init_miniconda` function to create the miniconda virtual environments for the scRNA-seq pipeline and ST pipeline of 10X Visium data and MERFISH data.
 
@@ -180,17 +176,3 @@ init_miniconda_stereo()
 ```
 
 
-
-## The installed packages with versions
-- R packages with versions
-```         
-Package	Version
-------- -------
-
-```
-- Python packages with versions
-```
-Package                  Version
------------------------- --------------
-
-```
diff --git a/.Rproj.user/F5A33326/sources/prop/68A8727B b/.Rproj.user/F5A33326/sources/prop/68A8727B
@@ -2,5 +2,5 @@
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diff --git a/01-HemaScope_installation_tutorial.Rmd b/01-HemaScope_installation_tutorial.Rmd
@@ -34,10 +34,6 @@ conda config --set show_channel_urls true
 
 ## Install R
 
-<<<<<<< Updated upstream
-<!-- - R 4.3.3 and python 3.9.12 -->
-=======
->>>>>>> Stashed changes
 - R 4.3.3
 
 ```
@@ -164,7 +160,7 @@ devtools::install_github(repo="ZhenyiWangTHU/HemaScopeR", dep = FALSE)
 <!-- # stereopy==1.3.1 -->
 <!-- ``` -->
 
-## Create the required python (v.3.9.12) virtual environment
+## Create the required python virtual environment
 
 -   Run the `init_miniconda` function to create the miniconda virtual environments for the scRNA-seq pipeline and ST pipeline of 10X Visium data and MERFISH data.
 
@@ -180,17 +176,3 @@ init_miniconda_stereo()
 ```
 
 
-
-## The installed packages with versions
-- R packages with versions
-```         
-Package	Version
-------- -------
-
-```
-- Python packages with versions
-```
-Package                  Version
------------------------- --------------
-
-```
diff --git a/_book/index.html b/_book/index.html
@@ -23,7 +23,7 @@
 <meta name="author" content="HemaScope team" />
 
 
-<meta name="date" content="2024-10-22" />
+<meta name="date" content="2024-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -147,8 +147,7 @@
 <li class="chapter" data-level="2.2" data-path="installation.html"><a href="installation.html#set-the-channels-in-conda"><i class="fa fa-check"></i><b>2.2</b> Set the channels in conda</a></li>
 <li class="chapter" data-level="2.3" data-path="installation.html"><a href="installation.html#install-r"><i class="fa fa-check"></i><b>2.3</b> Install R</a></li>
 <li class="chapter" data-level="2.4" data-path="installation.html"><a href="installation.html#install-required-r-packages"><i class="fa fa-check"></i><b>2.4</b> Install required R-packages</a></li>
-<li class="chapter" data-level="2.5" data-path="installation.html"><a href="installation.html#create-the-required-python-v.3.9.12-virtual-environment"><i class="fa fa-check"></i><b>2.5</b> Create the required python (v.3.9.12) virtual environment</a></li>
-<li class="chapter" data-level="2.6" data-path="installation.html"><a href="installation.html#the-installed-packages-with-versions"><i class="fa fa-check"></i><b>2.6</b> The installed packages with versions</a></li>
+<li class="chapter" data-level="2.5" data-path="installation.html"><a href="installation.html#create-the-required-python-virtual-environment"><i class="fa fa-check"></i><b>2.5</b> Create the required python virtual environment</a></li>
 </ul></li>
 <li class="chapter" data-level="3" data-path="integrated-scrna-seq-pipeline.html"><a href="integrated-scrna-seq-pipeline.html"><i class="fa fa-check"></i><b>3</b> Integrated scRNA-seq pipeline</a></li>
 <li class="chapter" data-level="4" data-path="step-by-step-scrna-seq-pipeline.html"><a href="step-by-step-scrna-seq-pipeline.html"><i class="fa fa-check"></i><b>4</b> Step-by-step scRNA-seq Pipeline</a>
@@ -348,7 +347,7 @@ <h1>
 <div id="header">
 <h1 class="title">HemaScope Tutorial</h1>
 <p class="author"><em>HemaScope team</em></p>
-<p class="date"><em>2024-10-22</em></p>
+<p class="date"><em>2024-10-25</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="2024-10-22" />
+<meta name="date" content="2024-10-25" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -147,8 +147,7 @@
 <li class="chapter" data-level="2.2" data-path="installation.html"><a href="installation.html#set-the-channels-in-conda"><i class="fa fa-check"></i><b>2.2</b> Set the channels in conda</a></li>
 <li class="chapter" data-level="2.3" data-path="installation.html"><a href="installation.html#install-r"><i class="fa fa-check"></i><b>2.3</b> Install R</a></li>
 <li class="chapter" data-level="2.4" data-path="installation.html"><a href="installation.html#install-required-r-packages"><i class="fa fa-check"></i><b>2.4</b> Install required R-packages</a></li>
-<li class="chapter" data-level="2.5" data-path="installation.html"><a href="installation.html#create-the-required-python-v.3.9.12-virtual-environment"><i class="fa fa-check"></i><b>2.5</b> Create the required python (v.3.9.12) virtual environment</a></li>
-<li class="chapter" data-level="2.6" data-path="installation.html"><a href="installation.html#the-installed-packages-with-versions"><i class="fa fa-check"></i><b>2.6</b> The installed packages with versions</a></li>
+<li class="chapter" data-level="2.5" data-path="installation.html"><a href="installation.html#create-the-required-python-virtual-environment"><i class="fa fa-check"></i><b>2.5</b> Create the required python virtual environment</a></li>
 </ul></li>
 <li class="chapter" data-level="3" data-path="integrated-scrna-seq-pipeline.html"><a href="integrated-scrna-seq-pipeline.html"><i class="fa fa-check"></i><b>3</b> Integrated scRNA-seq pipeline</a></li>
 <li class="chapter" data-level="4" data-path="step-by-step-scrna-seq-pipeline.html"><a href="step-by-step-scrna-seq-pipeline.html"><i class="fa fa-check"></i><b>4</b> Step-by-step scRNA-seq Pipeline</a>
@@ -377,11 +376,9 @@ <h2><span class="header-section-number">2.2</span> Set the channels in conda<a h
 </div>
 <div id="install-r" class="section level2 hasAnchor" number="2.3">
 <h2><span class="header-section-number">2.3</span> Install R<a href="installation.html#install-r" class="anchor-section" aria-label="Anchor link to header"></a></h2>
-<p>&lt;&lt;&lt;&lt;&lt;&lt;&lt; Updated upstream
-<!-- - R 4.3.3 and python 3.9.12 -->
-=======
-&gt;&gt;&gt;&gt;&gt;&gt;&gt; Stashed changes
-- R 4.3.3</p>
+<ul>
+<li>R 4.3.3</li>
+</ul>
 <pre><code>conda install R-base=4.3.3</code></pre>
 </div>
 <div id="install-required-r-packages" class="section level2 hasAnchor" number="2.4">
@@ -484,8 +481,8 @@ <h2><span class="header-section-number">2.4</span> Install required R-packages<a
 <!-- # stereopy==1.3.1 -->
 <!-- ``` -->
 </div>
-<div id="create-the-required-python-v.3.9.12-virtual-environment" class="section level2 hasAnchor" number="2.5">
-<h2><span class="header-section-number">2.5</span> Create the required python (v.3.9.12) virtual environment<a href="installation.html#create-the-required-python-v.3.9.12-virtual-environment" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<div id="create-the-required-python-virtual-environment" class="section level2 hasAnchor" number="2.5">
+<h2><span class="header-section-number">2.5</span> Create the required python virtual environment<a href="installation.html#create-the-required-python-virtual-environment" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <ul>
 <li>Run the <code>init_miniconda</code> function to create the miniconda virtual environments for the scRNA-seq pipeline and ST pipeline of 10X Visium data and MERFISH data.</li>
 </ul>
@@ -495,21 +492,6 @@ <h2><span class="header-section-number">2.5</span> Create the required python (v
 <li>(Optional) Run the <code>init_miniconda_stereo</code> function to create the miniconda virtual environment for the stereo-seq data.</li>
 </ul>
 <pre><code>init_miniconda_stereo()</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>
-<ul>
-<li>R packages with versions</li>
-</ul>
-<pre><code>Package Version
-------- -------
-</code></pre>
-<ul>
-<li>Python packages with versions</li>
-</ul>
-<pre><code>Package                  Version
------------------------- --------------
-</code></pre>
 
 </div>
 </div>