update documentation

_sources/installation/index.rst.txt

@@ -34,8 +34,9 @@ System Requirements
 ^^^^^^^^^^^^^^^^^^^
 
 - Operating system: macOS or Linux are highly recommended. CellOracle was developed and tested in Linux and macOS.
-- We found that the CellOracle calculations may be EXTREMELY SLOW in a Windows Subsystem for Linux (WSL). We do not recommend using WSL.
-- While you can install CellOracle using the Windows OS, please do so at your own risk and responsibility. We DO NOT provide any support for the use with the Windows OS.
+- CellOracle cannot be installed in Windows OS because some of the dependencies cannot be built on Windows OS.
+- It is possible to install CellOracle on a Windows Subsystem for Linux (WSL), but we found that the CellOracle calculations may be extremely slow on a WSL. We do not recommend using WSL.
+- While you can install CellOracle using the WSL, please do so at your own risk and responsibility. We DO NOT provide any support for the use with the Windows OS.
 
 - Memory: 16 G byte or more.  Memory usage also depends on the size of your scRNA-seq dataset. Please note that in silico perturbation, may require large amount of memory.
 - CPU: Core i5 or better processor. CellOracle's GRN inference function supports multicore calculation. Utilizing more CPU cores enables faster calculations.

installation/index.html

@@ -253,8 +253,9 @@ <h2>Install CellOracle<a class="headerlink" href="#install-celloracle" title="Pe
 <h3>System Requirements<a class="headerlink" href="#system-requirements" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li><p>Operating system: macOS or Linux are highly recommended. CellOracle was developed and tested in Linux and macOS.</p></li>
-<li><p>We found that the CellOracle calculations may be EXTREMELY SLOW in a Windows Subsystem for Linux (WSL). We do not recommend using WSL.</p></li>
-<li><p>While you can install CellOracle using the Windows OS, please do so at your own risk and responsibility. We DO NOT provide any support for the use with the Windows OS.</p></li>
+<li><p>CellOracle cannot be installed in Windows OS because some of the dependencies cannot be built on Windows OS.</p></li>
+<li><p>It is possible to install CellOracle on a Windows Subsystem for Linux (WSL), but we found that the CellOracle calculations may be extremely slow on a WSL. We do not recommend using WSL.</p></li>
+<li><p>While you can install CellOracle using the WSL, please do so at your own risk and responsibility. We DO NOT provide any support for the use with the Windows OS.</p></li>
 <li><p>Memory: 16 G byte or more.  Memory usage also depends on the size of your scRNA-seq dataset. Please note that in silico perturbation, may require large amount of memory.</p></li>
 <li><p>CPU: Core i5 or better processor. CellOracle’s GRN inference function supports multicore calculation. Utilizing more CPU cores enables faster calculations.</p></li>
 </ul>

modules/celloracle.html

@@ -370,7 +370,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>gois</strong> (<em>list of srt</em>) – List of gene name to highlight.</p></li>
 <li><p><strong>clusters</strong> (<em>list of str</em>) – List of cluster name to analyze. If None, all clusters in Links object will be analyzed.</p></li>
 <li><p><strong>scatter</strong> (<em>bool</em>) – Whether to make a scatter plot.</p></li>
@@ -395,7 +395,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>gois</strong> (<em>list of srt</em>) – List of gene name to highlight.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -412,7 +412,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>plot_model</strong> (<em>bool</em>) – Whether to plot linear approximation line.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -446,7 +446,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>value</strong> (<em>srt</em>) – The network score type.</p></li>
 <li><p><strong>cluster1</strong> (<em>str</em>) – Cluster name. Network scores in cluster1 will be visualized in the x-axis.</p></li>
 <li><p><strong>cluster2</strong> (<em>str</em>) – Cluster name. Network scores in cluster2 will be visualized in the y-axis.</p></li>
@@ -467,7 +467,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See Links class for details.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See Links class for details.</p></li>
 <li><p><strong>values</strong> (<em>list of str</em>) – The list of score to visualize. If it is None, all of the network score will be used.</p></li>
 <li><p><strong>method</strong> (<em>str</em>) – Plotting method. Select either “boxplot” or “barplot”.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -485,7 +485,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>goi</strong> (<em>srt</em>) – Gene name.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.</p></li>
@@ -501,7 +501,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>links</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
+<li><p><strong>links</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – See network_analysis.Links class for detail.</p></li>
 <li><p><strong>cluster</strong> (<em>str</em>) – Cluster name to analyze.</p></li>
 <li><p><strong>n_gene</strong> (<em>int</em>) – Number of genes to plot. Default is 50.</p></li>
 <li><p><strong>save</strong> (<em>str</em>) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -1068,7 +1068,7 @@ <h1>Custom class in celloracle<a class="headerlink" href="#custom-class-in-cello
 This function can be used to reconstruct GRNs based on pre-existing GRNs saved in Links object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>links_object</strong> (<a class="reference internal" href="#celloracle.Links" title="celloracle.Links"><em>Links</em></a>) – Please see the explanation of Links class.</p>
+<dd class="field-odd"><p><strong>links_object</strong> (<a class="reference internal" href="celloracle.network_analysis.html#celloracle.network_analysis.Links" title="celloracle.network_analysis.Links"><em>Links</em></a>) – Please see the explanation of Links class.</p>
 </dd>
 </dl>
 </dd></dl>