1. singleCellTK
  2. Commit a76fffb1da3bbeaff3a5060b8b663bc51f620935
Browse code

update docs

Yichen Wang authored on 20/10/2022 21:17:51
Showing 11 changed files
docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png
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docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png
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docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png
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docs/articles/heatmap.html
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... ... 
@@ -496,7 +496,7 @@ contains the identifiers users have, to <code>featureIndexBy</code> or
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 <code>cellIndexBy</code>. This specification allows directly giving one
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 column name of <code>rowData</code> or <code>colData</code>.</p>
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 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span><span class="va">subsetFeatureName</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu">rowData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">feature_name</span>, <span class="fl">50</span><span class="op">)</span></span>
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+<code class="sourceCode R"><span><span class="va">subsetFeatureName</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">feature_name</span>, <span class="fl">50</span><span class="op">)</span></span>
500 500 
 <span><span class="va">subsetCellBarcode</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">sce</span><span class="op">$</span><span class="va">cell_barcode</span>, <span class="fl">50</span><span class="op">)</span></span>
501 501 
 <span><span class="fu"><a href="../reference/plotSCEHeatmap.html">plotSCEHeatmap</a></span><span class="op">(</span>inSCE <span class="op">=</span> <span class="va">sce</span>, useAssay <span class="op">=</span> <span class="st">"counts"</span>, featureIndex <span class="op">=</span> <span class="va">subsetFeatureName</span>, featureIndexBy <span class="op">=</span> <span class="st">"feature_name"</span>, cellIndex <span class="op">=</span> <span class="va">subsetCellBarcode</span>, cellIndexBy <span class="op">=</span> <span class="st">"cell_barcode"</span><span class="op">)</span></span></code></pre></div>
502 502 
 <pre><code><span><span class="co">## dimnames(.) &lt;- NULL translated to</span></span>
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@@ -513,9 +513,9 @@ annotations. To make use of this functionality, pass a
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 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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 <code class="sourceCode R"><span><span class="co"># Make up arbitrary annotation, </span></span>
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 <span><span class="va">rowRandLabel</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">'aa'</span>, <span class="fl">100</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">'bb'</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span>
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-<span><span class="fu">rowData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">randLabel</span> <span class="op">&lt;-</span> <span class="va">rowRandLabel</span></span>
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+<span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">randLabel</span> <span class="op">&lt;-</span> <span class="va">rowRandLabel</span></span>
517 517 
 <span><span class="va">colRandLabel</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">'cc'</span>, <span class="fl">195</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">'dd'</span>, <span class="fl">195</span><span class="op">)</span><span class="op">)</span></span>
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-<span><span class="fu">colData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">randLabel</span> <span class="op">&lt;-</span> <span class="va">colRandLabel</span></span>
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+<span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">colData</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">randLabel</span> <span class="op">&lt;-</span> <span class="va">colRandLabel</span></span>
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 <span><span class="fu"><a href="../reference/plotSCEHeatmap.html">plotSCEHeatmap</a></span><span class="op">(</span>inSCE <span class="op">=</span> <span class="va">sce</span>, useAssay <span class="op">=</span> <span class="st">"counts"</span>, featureIndex <span class="op">=</span> <span class="va">featureSubset</span>, cellIndex <span class="op">=</span> <span class="va">cellSubset</span>, rowDataName <span class="op">=</span> <span class="st">"randLabel"</span>, colDataName <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"type"</span>, <span class="st">"randLabel"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
520 520 
 <pre><code><span><span class="co">## dimnames(.) &lt;- NULL translated to</span></span>
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 <span><span class="co">## dimnames(.) &lt;- list(NULL,NULL)</span></span>
docs/pkgdown.yml
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@@ -32,5 +32,5 @@ articles:
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   ui_qc: ui_qc.html
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   visualization: visualization.html
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   singleCellTK: singleCellTK.html
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-last_built: 2022-10-18T19:02Z
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+last_built: 2022-10-20T20:53Z
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docs/reference/getFindMarkerTopTable.html
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@@ -282,9 +282,9 @@ function to extract a top marker table.</p>
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 <span class="r-in"><span><span class="va">mouseBrainSubsetSCE</span> <span class="op">&lt;-</span> <span class="fu"><a href="runFindMarker.html">runFindMarker</a></span><span class="op">(</span><span class="va">mouseBrainSubsetSCE</span>,</span></span>
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 <span class="r-in"><span>                                     useAssay <span class="op">=</span> <span class="st">"logcounts"</span>,</span></span>
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 <span class="r-in"><span>                                     cluster <span class="op">=</span> <span class="st">"level1class"</span><span class="op">)</span></span></span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:16:34 2022 ... Identifying markers for cluster 'microglia', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:16:34 2022 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:16:35 2022 ... Organizing findMarker result</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:32 2022 ... Identifying markers for cluster 'microglia', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:33 2022 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:34 2022 ... Organizing findMarker result</span>
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 <span class="r-in"><span><span class="fu">getFindMarkerTopTable</span><span class="op">(</span><span class="va">mouseBrainSubsetSCE</span><span class="op">)</span></span></span>
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 <span class="r-out co"><span class="r-pr">#&gt;</span>        Gene  Log2_FC       Pvalue          FDR      level1class clusterExprPerc</span>
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 <span class="r-out co"><span class="r-pr">#&gt;</span> 1228   Apoe 4.439115 3.642815e-06 0.0001796628        microglia       1.0000000</span>
docs/reference/index.html
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... ... 
@@ -664,7 +664,7 @@ object</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotFindMarkerHeatmap.html">plotFindMarkerHeatmap()</a></code> <code><a href="plotFindMarkerHeatmap.html">plotMarkerDiffExp()</a></code> </p>
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         </td>
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-        <td><p>Plot a heatmap to visualize the result of <code><a href="https://rdrr.io/pkg/singleCellTK/man/runFindMarker.html" class="external-link">runFindMarker</a></code></p></td>
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+        <td><p>Plot a heatmap to visualize the result of <code>runFindMarker</code></p></td>
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       </tr></tbody><tbody><tr><th colspan="2">
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           <h2 id="differential-abundance">Differential Abundance <a href="#differential-abundance" class="anchor" aria-hidden="true"></a></h2>
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           <p class="section-desc"></p>
... ... 
@@ -708,7 +708,7 @@ object</p></td>
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       </tr><tr><td>
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           <p><code><a href="runGSVA.html">runGSVA()</a></code> </p>
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         </td>
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-        <td><p>Run GSVA analysis on a <a href="https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html" class="external-link">SingleCellExperiment</a> object</p></td>
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+        <td><p>Run GSVA analysis on a SingleCellExperiment object</p></td>
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       </tr><tr><td>
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           <p><code><a href="runVAM.html">runVAM()</a></code> </p>
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         </td>
... ... 
@@ -740,7 +740,7 @@ object</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotTSCANClusterDEG.html">plotTSCANClusterDEG()</a></code> </p>
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         </td>
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-        <td><p>Plot features identified by <code><a href="https://rdrr.io/pkg/singleCellTK/man/runTSCANClusterDEAnalysis.html" class="external-link">runTSCANClusterDEAnalysis</a></code> on
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+        <td><p>Plot features identified by <code>runTSCANClusterDEAnalysis</code> on
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 cell 2D embedding with MST overlaid</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotTSCANClusterPseudo.html">plotTSCANClusterPseudo()</a></code> </p>
... ... 
@@ -923,7 +923,7 @@ and UMAP</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotFindMarkerHeatmap.html">plotFindMarkerHeatmap()</a></code> <code><a href="plotFindMarkerHeatmap.html">plotMarkerDiffExp()</a></code> </p>
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         </td>
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-        <td><p>Plot a heatmap to visualize the result of <code><a href="https://rdrr.io/pkg/singleCellTK/man/runFindMarker.html" class="external-link">runFindMarker</a></code></p></td>
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+        <td><p>Plot a heatmap to visualize the result of <code>runFindMarker</code></p></td>
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       </tr><tr><td>
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           <p><code><a href="plotMASTThresholdGenes.html">plotMASTThresholdGenes()</a></code> </p>
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         </td>
... ... 
@@ -1044,7 +1044,7 @@ Plots the selected dimensionality reduction method</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotTSCANClusterDEG.html">plotTSCANClusterDEG()</a></code> </p>
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         </td>
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-        <td><p>Plot features identified by <code><a href="https://rdrr.io/pkg/singleCellTK/man/runTSCANClusterDEAnalysis.html" class="external-link">runTSCANClusterDEAnalysis</a></code> on
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+        <td><p>Plot features identified by <code>runTSCANClusterDEAnalysis</code> on
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 cell 2D embedding with MST overlaid</p></td>
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       </tr><tr><td>
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           <p><code><a href="plotTSCANClusterPseudo.html">plotTSCANClusterPseudo()</a></code> </p>
... ... 
@@ -1399,7 +1399,7 @@ multiple conditions, respectively.</p></td>
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       </tr><tr><td>
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           <p><code><a href="summarizeSCE.html">summarizeSCE()</a></code> </p>
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         </td>
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-        <td><p>Summarize an assay in a <a href="https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html" class="external-link">SingleCellExperiment</a></p></td>
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+        <td><p>Summarize an assay in a SingleCellExperiment</p></td>
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       </tr></tbody><tbody><tr><th colspan="2">
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           <h2 id="python-environment-setting">Python Environment Setting <a href="#python-environment-setting" class="anchor" aria-hidden="true"></a></h2>
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           <p class="section-desc"></p>
docs/reference/plotFindMarkerHeatmap.html
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@@ -417,9 +417,9 @@ auto generated annotation for this plot.</p></dd>
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 <span class="r-in"><span><span class="fu">logcounts</span><span class="op">(</span><span class="va">sceBatches</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log1p</a></span><span class="op">(</span><span class="fu">counts</span><span class="op">(</span><span class="va">sceBatches</span><span class="op">)</span><span class="op">)</span></span></span>
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 <span class="r-in"><span><span class="va">sce.w</span> <span class="op">&lt;-</span> <span class="fu"><a href="subsetSCECols.html">subsetSCECols</a></span><span class="op">(</span><span class="va">sceBatches</span>, colData <span class="op">=</span> <span class="st">"batch == 'w'"</span><span class="op">)</span></span></span>
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 <span class="r-in"><span><span class="va">sce.w</span> <span class="op">&lt;-</span> <span class="fu"><a href="runFindMarker.html">runFindMarker</a></span><span class="op">(</span><span class="va">sce.w</span>, method <span class="op">=</span> <span class="st">"wilcox"</span>, cluster <span class="op">=</span> <span class="st">"cell_type"</span><span class="op">)</span></span></span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:19:11 2022 ... Identifying markers for cluster 'beta', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:19:11 2022 ... Identifying markers for cluster 'alpha', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:19:12 2022 ... Organizing findMarker result</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:34 2022 ... Identifying markers for cluster 'beta', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:35 2022 ... Identifying markers for cluster 'alpha', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:35 2022 ... Organizing findMarker result</span>
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 <span class="r-in"><span><span class="fu">plotFindMarkerHeatmap</span><span class="op">(</span><span class="va">sce.w</span><span class="op">)</span></span></span>
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 <span class="r-plt img"><img src="plotFindMarkerHeatmap-1.png" alt="" width="700" height="433"></span>
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 </code></pre></div>
docs/reference/runFindMarker.html
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@@ -339,9 +339,9 @@ than <code>detectThresh</code> in the control cell group.</p>
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 <span class="r-in"><span><span class="va">mouseBrainSubsetSCE</span> <span class="op">&lt;-</span> <span class="fu">runFindMarker</span><span class="op">(</span><span class="va">mouseBrainSubsetSCE</span>,</span></span>
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 <span class="r-in"><span>                                     useAssay <span class="op">=</span> <span class="st">"logcounts"</span>,</span></span>
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 <span class="r-in"><span>                                     cluster <span class="op">=</span> <span class="st">"level1class"</span><span class="op">)</span></span></span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:22:01 2022 ... Identifying markers for cluster 'microglia', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:22:02 2022 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox'</span>
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-<span class="r-msg co"><span class="r-pr">#&gt;</span> Wed Oct 19 03:22:02 2022 ... Organizing findMarker result</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:38 2022 ... Identifying markers for cluster 'microglia', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:38 2022 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox'</span>
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+<span class="r-msg co"><span class="r-pr">#&gt;</span> Thu Oct 20 16:53:39 2022 ... Organizing findMarker result</span>
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 </code></pre></div>
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     </div>
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   </div>
docs/sitemap.xml
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+    <loc>/LICENSE-text.html</loc>
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+    <loc>/articles/cnsl_cellqc.html</loc>
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+  <url>
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+    <loc>/articles/seurat_curated_workflow.html</loc>
89 
+  </url>
87 90 
   <url>
88 91 
     <loc>/articles/singleCellTK.html</loc>
89 92 
   </url>
93 
+  <url>
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+    <loc>/articles/trajectoryAnalysis.html</loc>
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+  </url>
90 96 
   <url>
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     <loc>/articles/ui_qc.html</loc>
92 98 
   </url>
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@@ -100,10 +106,19 @@
100 106 
     <loc>/index.html</loc>
101 107 
   </url>
102 108 
   <url>
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-    <loc>/LICENSE-text.html</loc>
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+    <loc>/news/index.html</loc>
104 110 
   </url>
105 111 
   <url>
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-    <loc>/news/index.html</loc>
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+    <loc>/reference/MitoGenes.html</loc>
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+  </url>
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+  <url>
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+    <loc>/reference/SCtkExperiment-class.html</loc>
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+  </url>
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+  <url>
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+    <loc>/reference/SCtkExperiment.html</loc>
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+  </url>
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+  <url>
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+    <loc>/reference/SEG.html</loc>
107 122 
   </url>
108 123 
   <url>
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     <loc>/reference/alignSingleCellData.html</loc>
... ... 
@@ -132,9 +147,6 @@
132 147 
   <url>
133 148 
     <loc>/reference/convertSeuratToSCE.html</loc>
134 149 
   </url>
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-  <url>
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-    <loc>/reference/dataAnnotationColor.html</loc>
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-  </url>
138 150 
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     <loc>/reference/dedupRowNames.html</loc>
140 152 
   </url>
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@@ -150,48 +162,6 @@
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   <url>
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     <loc>/reference/distinctColors.html</loc>
152 164 
   </url>
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-  <url>
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-    <loc>/reference/dot-addSeuratToMetaDataSCE.html</loc>
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-  </url>
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-  <url>
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-    <loc>/reference/dot-checkDiffExpResultExists.html</loc>
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-  </url>
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-  <url>
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-    <loc>/reference/dot-computeSignificantPC.html</loc>
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-  </url>
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-  <url>
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-    <loc>/reference/dot-extractSCEAnnotation.html</loc>
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-  </url>
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-  <url>
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-    <loc>/reference/dot-formatDEAList.html</loc>
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-  </url>
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-  <url>
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-    <loc>/reference/dot-getComponentNames.html</loc>
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-    <loc>/reference/dot-ggBar.html</loc>
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-    <loc>/reference/dot-ggDensity.html</loc>
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-    <loc>/reference/dot-ggViolin.html</loc>
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-  </url>
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-    <loc>/reference/dot-sce2adata.html</loc>
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-  </url>
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-    <loc>/reference/dot-seuratGetVariableFeatures.html</loc>
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-  </url>
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-  </url>
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-    <loc>/reference/dot-updateAssaySCE.html</loc>
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-  </url>
195 165 
   <url>
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     <loc>/reference/downSampleCells.html</loc>
197 167 
   </url>
... ... 
@@ -220,22 +190,22 @@
220 190 
     <loc>/reference/expDeleteDataTag.html</loc>
221 191 
   </url>
222 192 
   <url>
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-    <loc>/reference/exportSCE.html</loc>
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+    <loc>/reference/expSetDataTag.html</loc>
224 194 
   </url>
225 195 
   <url>
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-    <loc>/reference/exportSCEtoAnnData.html</loc>
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+    <loc>/reference/expTaggedData.html</loc>
227 197 
   </url>
228 198 
   <url>
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-    <loc>/reference/exportSCEtoFlatFile.html</loc>
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+    <loc>/reference/exportSCE.html</loc>
230 200 
   </url>
231 201 
   <url>
232 202 
     <loc>/reference/exportSCEToSeurat.html</loc>
233 203 
   </url>
234 204 
   <url>
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-    <loc>/reference/expSetDataTag.html</loc>
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+    <loc>/reference/exportSCEtoAnnData.html</loc>
236 206 
   </url>
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   <url>
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-    <loc>/reference/expTaggedData.html</loc>
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+    <loc>/reference/exportSCEtoFlatFile.html</loc>
239 209 
   </url>
240 210 
   <url>
241 211 
     <loc>/reference/featureIndex.html</loc>
... ... 
@@ -276,6 +246,9 @@
276 246 
   <url>
277 247 
     <loc>/reference/getEnrichRResult.html</loc>
278 248 
   </url>
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+  <url>
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+    <loc>/reference/getFindMarkerTopTable.html</loc>
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+  </url>
279 252 
   <url>
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     <loc>/reference/getGenesetNamesFromCollection.html</loc>
281 254 
   </url>
... ... 
@@ -297,15 +270,15 @@
297 270 
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     <loc>/reference/getSoupX.html</loc>
299 272 
   </url>
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-  </url>
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   <url>
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     <loc>/reference/getTSCANResults.html</loc>
305 275 
   </url>
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   <url>
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     <loc>/reference/getTSNE.html</loc>
308 278 
   </url>
279 
+  <url>
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+    <loc>/reference/getTopHVG.html</loc>
281 
+  </url>
309 282 
   <url>
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     <loc>/reference/getUMAP.html</loc>
311 284 
   </url>
... ... 
@@ -375,9 +348,6 @@
375 348 
   <url>
376 349 
     <loc>/reference/mergeSCEColData.html</loc>
377 350 
   </url>
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-  <url>
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-    <loc>/reference/MitoGenes.html</loc>
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381 351 
   <url>
382 352 
     <loc>/reference/mouseBrainSubsetSCE.html</loc>
383 353 
   </url>
... ... 
@@ -420,9 +390,6 @@
420 390 
   <url>
421 391 
     <loc>/reference/plotCxdsResults.html</loc>
422 392 
   </url>
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-  <url>
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-    <loc>/reference/plotDecontXResults.html</loc>
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-  </url>
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   <url>
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     <loc>/reference/plotDEGHeatmap.html</loc>
428 395 
   </url>
... ... 
@@ -435,6 +402,9 @@
435 402 
   <url>
436 403 
     <loc>/reference/plotDEGVolcano.html</loc>
437 404 
   </url>
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+  <url>
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+    <loc>/reference/plotDecontXResults.html</loc>
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+  </url>
438 408 
   <url>
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     <loc>/reference/plotDimRed.html</loc>
440 410 
   </url>
... ... 
@@ -451,25 +421,22 @@
451 421 
     <loc>/reference/plotEmptyDropsScatter.html</loc>
452 422 
   </url>
453 423 
   <url>
454 
-    <loc>/reference/plotMarkerDiffExp.html</loc>
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+    <loc>/reference/plotFindMarkerHeatmap.html</loc>
455 425 
   </url>
456 426 
   <url>
457 427 
     <loc>/reference/plotMASTThresholdGenes.html</loc>
458 428 
   </url>
459 429 
   <url>
460 
-    <loc>/reference/plotPathway.html</loc>
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+    <loc>/reference/plotMarkerDiffExp.html</loc>
461 431 
   </url>
462 432 
   <url>
463 433 
     <loc>/reference/plotPCA.html</loc>
464 434 
   </url>
465 435 
   <url>
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-    <loc>/reference/plotRunPerCellQCResults.html</loc>
467 
-  </url>
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-  <url>
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-    <loc>/reference/plotScDblFinderResults.html</loc>
436 
+    <loc>/reference/plotPathway.html</loc>
470 437 
   </url>
471 438 
   <url>
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-    <loc>/reference/plotScdsHybridResults.html</loc>
439 
+    <loc>/reference/plotRunPerCellQCResults.html</loc>
473 440 
   </url>
474 441 
   <url>
475 442 
     <loc>/reference/plotSCEBarAssayData.html</loc>
... ... 
@@ -510,6 +477,12 @@
510 477 
   <url>
511 478 
     <loc>/reference/plotSCEViolinColData.html</loc>
512 479 
   </url>
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+  <url>
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+    <loc>/reference/plotScDblFinderResults.html</loc>
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+  </url>
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+  <url>
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+    <loc>/reference/plotScdsHybridResults.html</loc>
485 
+  </url>
513 486 
   <url>
514 487 
     <loc>/reference/plotScrubletResults.html</loc>
515 488 
   </url>
... ... 
@@ -520,10 +493,10 @@
520 493 
     <loc>/reference/plotSeuratGenes.html</loc>
521 494 
   </url>
522 495 
   <url>
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-    <loc>/reference/plotSeuratHeatmap.html</loc>
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+    <loc>/reference/plotSeuratHVG.html</loc>
524 497 
   </url>
525 498 
   <url>
526 
-    <loc>/reference/plotSeuratHVG.html</loc>
499 
+    <loc>/reference/plotSeuratHeatmap.html</loc>
527 500 
   </url>
528 501 
   <url>
529 502 
     <loc>/reference/plotSeuratJackStraw.html</loc>
... ... 
@@ -535,11 +508,17 @@
535 508 
     <loc>/reference/plotSoupXResults.html</loc>
536 509 
   </url>
537 510 
   <url>
538 
-    <loc>/reference/plotTopHVG.html</loc>
511 
+    <loc>/reference/plotTSCANClusterDEG.html</loc>
512 
+  </url>
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+  <url>
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+    <loc>/reference/plotTSCANClusterPseudo.html</loc>
539 515 
   </url>
540 516 
   <url>
541 517 
     <loc>/reference/plotTSCANDEgenes.html</loc>
542 518 
   </url>
519 
+  <url>
520 
+    <loc>/reference/plotTSCANDimReduceFeatures.html</loc>
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+  </url>
543 522 
   <url>
544 523 
     <loc>/reference/plotTSCANPseudotimeGenes.html</loc>
545 524 
   </url>
... ... 
@@ -552,6 +531,9 @@
552 531 
   <url>
553 532 
     <loc>/reference/plotTSNE.html</loc>
554 533 
   </url>
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+  <url>
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+    <loc>/reference/plotTopHVG.html</loc>
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+  </url>
555 537 
   <url>
556 538 
     <loc>/reference/plotUMAP.html</loc>
557 539 
   </url>
... ... 
@@ -613,10 +595,10 @@
613 595 
     <loc>/reference/retrieveSCEIndex.html</loc>
614 596 
   </url>
615 597 
   <url>
616 
-    <loc>/reference/runBarcodeRankDrops.html</loc>
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+    <loc>/reference/runBBKNN.html</loc>
617 599 
   </url>
618 600 
   <url>
619 
-    <loc>/reference/runBBKNN.html</loc>
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+    <loc>/reference/runBarcodeRankDrops.html</loc>
620 602 
   </url>
621 603 
   <url>
622 604 
     <loc>/reference/runBcds.html</loc>
... ... 
@@ -666,6 +648,9 @@
666 648 
   <url>
667 649 
     <loc>/reference/runFeatureSelection.html</loc>
668 650 
   </url>
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+  <url>
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+    <loc>/reference/runFindMarker.html</loc>
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+  </url>
669 654 
   <url>
670 655 
     <loc>/reference/runGSVA.html</loc>
671 656 
   </url>
... ... 
@@ -684,6 +669,9 @@
684 669 
   <url>
685 670 
     <loc>/reference/runMNNCorrect.html</loc>
686 671 
   </url>
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+  <url>
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+    <loc>/reference/runModelGeneVar.html</loc>
674 
+  </url>
687 675 
   <url>
688 676 
     <loc>/reference/runNormalization.html</loc>
689 677 
   </url>
... ... 
@@ -693,15 +681,15 @@
693 681 
   <url>
694 682 
     <loc>/reference/runSCANORAMA.html</loc>
695 683 
   </url>
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-  <url>
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-    <loc>/reference/runScDblFinder.html</loc>
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-  </url>
699 684 
   <url>
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     <loc>/reference/runSCGEN.html</loc>
701 686 
   </url>
702 687 
   <url>
703 688 
     <loc>/reference/runSCMerge.html</loc>
704 689 
   </url>
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+  <url>
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+    <loc>/reference/runScDblFinder.html</loc>
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+  </url>
705 693 
   <url>
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     <loc>/reference/runScranSNN.html</loc>
707 695 
   </url>
... ... 
@@ -742,10 +730,10 @@
742 730 
     <loc>/reference/runSeuratPCA.html</loc>
743 731 
   </url>
744 732 
   <url>
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-    <loc>/reference/runSeuratScaleData.html</loc>
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+    <loc>/reference/runSeuratSCTransform.html</loc>
746 734 
   </url>
747 735 
   <url>
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-    <loc>/reference/runSeuratSCTransform.html</loc>
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+    <loc>/reference/runSeuratScaleData.html</loc>
749 737 
   </url>
750 738 
   <url>
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     <loc>/reference/runSeuratTSNE.html</loc>
... ... 
@@ -768,6 +756,12 @@
768 756 
   <url>
769 757 
     <loc>/reference/runTSCANDEG.html</loc>
770 758 
   </url>
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+  <url>
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+    <loc>/reference/runTSNE.html</loc>
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+  </url>
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+    <loc>/reference/runUMAP.html</loc>
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   <url>
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     <loc>/reference/runVAM.html</loc>
773 767 
   </url>
... ... 
@@ -780,15 +774,15 @@
780 774 
   <url>
781 775 
     <loc>/reference/scaterCPM.html</loc>
782 776 
   </url>
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-  <url>
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-  </url>
786 777 
   <url>
787 778 
     <loc>/reference/scaterPCA.html</loc>
788 779 
   </url>
789 780 
   <url>
790 781 
     <loc>/reference/scater_logNormCounts.html</loc>
791 782 
   </url>
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+  <url>
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+    <loc>/reference/scaterlogNormCounts.html</loc>
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+  </url>
792 786 
   <url>
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     <loc>/reference/sce.html</loc>
794 788 
   </url>
... ... 
@@ -801,12 +795,6 @@
801 795 
   <url>
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     <loc>/reference/scran_modelGeneVar.html</loc>
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   </url>
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-  <url>
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-  </url>
810 798 
   <url>
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     <loc>/reference/sctkListGeneSetCollections.html</loc>
812 800 
   </url>
... ... 
@@ -816,9 +804,6 @@
816 804 
   <url>
817 805 
     <loc>/reference/sctkPythonInstallVirtualEnv.html</loc>
818 806 
   </url>
819 
-  <url>
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-    <loc>/reference/SEG.html</loc>
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-  </url>
822 807 
   <url>
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     <loc>/reference/selectSCTKConda.html</loc>
824 809 
   </url>
... ... 
@@ -829,10 +814,10 @@
829 814 
     <loc>/reference/setRowNames.html</loc>
830 815 
   </url>
831 816 
   <url>
832 
-    <loc>/reference/setSampleSummaryStatsTable-set.html</loc>
817 
+    <loc>/reference/setSCTKDisplayRow.html</loc>
833 818 
   </url>
834 819 
   <url>
835 
-    <loc>/reference/setSCTKDisplayRow.html</loc>
820 
+    <loc>/reference/setSampleSummaryStatsTable-set.html</loc>
836 821 
   </url>
837 822 
   <url>
838 823 
     <loc>/reference/simpleLog.html</loc>