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@@ -314,8 +314,25 @@
 <li class="chapter" data-level="11.8.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#hierarchical-clustering"><i class="fa fa-check"></i><b>11.8.3</b> Hierarchical clustering</a></li>
 <li class="chapter" data-level="11.8.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#subclustering"><i class="fa fa-check"></i><b>11.8.4</b> Subclustering</a></li>
 </ul></li>
-<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a></li>
-<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a></li>
+<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a>
+<ul>
+<li class="chapter" data-level="11.9.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#scoring-markers-by-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.1</b> Scoring markers by pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#effect-sizes-for-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.2</b> Effect sizes for pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#summaries-of-pairwise-effects"><i class="fa fa-check"></i><b>11.9.3</b> Summaries of pairwise effects</a></li>
+<li class="chapter" data-level="11.9.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#choose-top-markers"><i class="fa fa-check"></i><b>11.9.4</b> Choose top markers</a></li>
+<li class="chapter" data-level="11.9.5" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#handling-blocking-factors"><i class="fa fa-check"></i><b>11.9.5</b> Handling blocking factors</a></li>
+<li class="chapter" data-level="11.9.6" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#deconvobuddies"><i class="fa fa-check"></i><b>11.9.6</b> Deconvobuddies</a></li>
+</ul></li>
+<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a>
+<ul>
+<li class="chapter" data-level="11.10.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-reference-data"><i class="fa fa-check"></i><b>11.10.1</b> Assigning cell labels from reference data</a></li>
+</ul></li>
+<li class="chapter" data-level="11.11" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#getting-ready-again"><i class="fa fa-check"></i><b>11.11</b> Getting ready again</a>
+<ul>
+<li class="chapter" data-level="11.11.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#using-existing-references"><i class="fa fa-check"></i><b>11.11.1</b> Using existing references</a></li>
+<li class="chapter" data-level="11.11.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-gene-sets"><i class="fa fa-check"></i><b>11.11.2</b> Assigning cell labels from gene sets</a></li>
+</ul></li>
+<li class="chapter" data-level="11.12" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#references-4"><i class="fa fa-check"></i><b>11.12</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="12" data-path="introduction-to-spatial-transcriptomics.html"><a href="introduction-to-spatial-transcriptomics.html"><i class="fa fa-check"></i><b>12</b> Introduction to spatial transcriptomics</a>
 <ul>
@@ -363,7 +380,7 @@
 <li class="chapter" data-level="14.6.4" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#edit-with-your-information"><i class="fa fa-check"></i><b>14.6.4</b> Edit with Your Information</a></li>
 <li class="chapter" data-level="14.6.5" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#deploy-the-page"><i class="fa fa-check"></i><b>14.6.5</b> Deploy the Page</a></li>
 </ul></li>
-<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-4"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
+<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-5"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="final-r-session.html"><a href="final-r-session.html"><i class="fa fa-check"></i>Final R Session</a></li>
 </ul>

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diff --git a/biocthis-introduction.html b/biocthis-introduction.html
@@ -314,8 +314,25 @@
 <li class="chapter" data-level="11.8.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#hierarchical-clustering"><i class="fa fa-check"></i><b>11.8.3</b> Hierarchical clustering</a></li>
 <li class="chapter" data-level="11.8.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#subclustering"><i class="fa fa-check"></i><b>11.8.4</b> Subclustering</a></li>
 </ul></li>
-<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a></li>
-<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a></li>
+<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a>
+<ul>
+<li class="chapter" data-level="11.9.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#scoring-markers-by-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.1</b> Scoring markers by pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#effect-sizes-for-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.2</b> Effect sizes for pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#summaries-of-pairwise-effects"><i class="fa fa-check"></i><b>11.9.3</b> Summaries of pairwise effects</a></li>
+<li class="chapter" data-level="11.9.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#choose-top-markers"><i class="fa fa-check"></i><b>11.9.4</b> Choose top markers</a></li>
+<li class="chapter" data-level="11.9.5" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#handling-blocking-factors"><i class="fa fa-check"></i><b>11.9.5</b> Handling blocking factors</a></li>
+<li class="chapter" data-level="11.9.6" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#deconvobuddies"><i class="fa fa-check"></i><b>11.9.6</b> Deconvobuddies</a></li>
+</ul></li>
+<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a>
+<ul>
+<li class="chapter" data-level="11.10.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-reference-data"><i class="fa fa-check"></i><b>11.10.1</b> Assigning cell labels from reference data</a></li>
+</ul></li>
+<li class="chapter" data-level="11.11" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#getting-ready-again"><i class="fa fa-check"></i><b>11.11</b> Getting ready again</a>
+<ul>
+<li class="chapter" data-level="11.11.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#using-existing-references"><i class="fa fa-check"></i><b>11.11.1</b> Using existing references</a></li>
+<li class="chapter" data-level="11.11.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-gene-sets"><i class="fa fa-check"></i><b>11.11.2</b> Assigning cell labels from gene sets</a></li>
+</ul></li>
+<li class="chapter" data-level="11.12" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#references-4"><i class="fa fa-check"></i><b>11.12</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="12" data-path="introduction-to-spatial-transcriptomics.html"><a href="introduction-to-spatial-transcriptomics.html"><i class="fa fa-check"></i><b>12</b> Introduction to spatial transcriptomics</a>
 <ul>
@@ -363,7 +380,7 @@
 <li class="chapter" data-level="14.6.4" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#edit-with-your-information"><i class="fa fa-check"></i><b>14.6.4</b> Edit with Your Information</a></li>
 <li class="chapter" data-level="14.6.5" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#deploy-the-page"><i class="fa fa-check"></i><b>14.6.5</b> Deploy the Page</a></li>
 </ul></li>
-<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-4"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
+<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-5"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="final-r-session.html"><a href="final-r-session.html"><i class="fa fa-check"></i>Final R Session</a></li>
 </ul>
@@ -447,9 +464,9 @@ <h3><span class="header-section-number">10.3.1</span> Example function<a href="b
 <span id="cb118-4"><a href="biocthis-introduction.html#cb118-4" tabindex="-1"></a>    <span class="fu">paste0</span>(date_weekday, <span class="st">&quot;: &quot;</span>, praise<span class="sc">::</span><span class="fu">praise</span>())</span>
 <span id="cb118-5"><a href="biocthis-introduction.html#cb118-5" tabindex="-1"></a>}</span>
 <span id="cb118-6"><a href="biocthis-introduction.html#cb118-6" tabindex="-1"></a><span class="fu">weekday_praise</span>()</span>
-<span id="cb118-7"><a href="biocthis-introduction.html#cb118-7" tabindex="-1"></a><span class="co">#&gt; [1] &quot;Monday: You are exquisite!&quot;</span></span></code></pre></div>
+<span id="cb118-7"><a href="biocthis-introduction.html#cb118-7" tabindex="-1"></a><span class="co">#&gt; [1] &quot;Tuesday: You are super!&quot;</span></span></code></pre></div>
 <div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb119-1"><a href="biocthis-introduction.html#cb119-1" tabindex="-1"></a><span class="fu">weekday_praise</span>(<span class="st">&quot;2024-06-09&quot;</span>)</span>
-<span id="cb119-2"><a href="biocthis-introduction.html#cb119-2" tabindex="-1"></a><span class="co">#&gt; [1] &quot;Sunday: You are brilliant!&quot;</span></span></code></pre></div>
+<span id="cb119-2"><a href="biocthis-introduction.html#cb119-2" tabindex="-1"></a><span class="co">#&gt; [1] &quot;Sunday: You are dandy!&quot;</span></span></code></pre></div>
 <p>Here’s the full code for the function and its documentation.</p>
 <div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb120-1"><a href="biocthis-introduction.html#cb120-1" tabindex="-1"></a><span class="co">#&#39; Praise a weekday</span></span>
 <span id="cb120-2"><a href="biocthis-introduction.html#cb120-2" tabindex="-1"></a><span class="co">#&#39;</span></span>

diff --git a/dge-model-building-with-variancepartition.html b/dge-model-building-with-variancepartition.html
@@ -314,8 +314,25 @@
 <li class="chapter" data-level="11.8.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#hierarchical-clustering"><i class="fa fa-check"></i><b>11.8.3</b> Hierarchical clustering</a></li>
 <li class="chapter" data-level="11.8.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#subclustering"><i class="fa fa-check"></i><b>11.8.4</b> Subclustering</a></li>
 </ul></li>
-<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a></li>
-<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a></li>
+<li class="chapter" data-level="11.9" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#marker-gene-detection"><i class="fa fa-check"></i><b>11.9</b> Marker gene detection</a>
+<ul>
+<li class="chapter" data-level="11.9.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#scoring-markers-by-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.1</b> Scoring markers by pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#effect-sizes-for-pairwise-comparisons"><i class="fa fa-check"></i><b>11.9.2</b> Effect sizes for pairwise comparisons</a></li>
+<li class="chapter" data-level="11.9.3" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#summaries-of-pairwise-effects"><i class="fa fa-check"></i><b>11.9.3</b> Summaries of pairwise effects</a></li>
+<li class="chapter" data-level="11.9.4" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#choose-top-markers"><i class="fa fa-check"></i><b>11.9.4</b> Choose top markers</a></li>
+<li class="chapter" data-level="11.9.5" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#handling-blocking-factors"><i class="fa fa-check"></i><b>11.9.5</b> Handling blocking factors</a></li>
+<li class="chapter" data-level="11.9.6" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#deconvobuddies"><i class="fa fa-check"></i><b>11.9.6</b> Deconvobuddies</a></li>
+</ul></li>
+<li class="chapter" data-level="11.10" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#cell-type-annotation"><i class="fa fa-check"></i><b>11.10</b> Cell type annotation</a>
+<ul>
+<li class="chapter" data-level="11.10.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-reference-data"><i class="fa fa-check"></i><b>11.10.1</b> Assigning cell labels from reference data</a></li>
+</ul></li>
+<li class="chapter" data-level="11.11" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#getting-ready-again"><i class="fa fa-check"></i><b>11.11</b> Getting ready again</a>
+<ul>
+<li class="chapter" data-level="11.11.1" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#using-existing-references"><i class="fa fa-check"></i><b>11.11.1</b> Using existing references</a></li>
+<li class="chapter" data-level="11.11.2" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#assigning-cell-labels-from-gene-sets"><i class="fa fa-check"></i><b>11.11.2</b> Assigning cell labels from gene sets</a></li>
+</ul></li>
+<li class="chapter" data-level="11.12" data-path="scrna-seq-data-analysis-overview.html"><a href="scrna-seq-data-analysis-overview.html#references-4"><i class="fa fa-check"></i><b>11.12</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="12" data-path="introduction-to-spatial-transcriptomics.html"><a href="introduction-to-spatial-transcriptomics.html"><i class="fa fa-check"></i><b>12</b> Introduction to spatial transcriptomics</a>
 <ul>
@@ -363,7 +380,7 @@
 <li class="chapter" data-level="14.6.4" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#edit-with-your-information"><i class="fa fa-check"></i><b>14.6.4</b> Edit with Your Information</a></li>
 <li class="chapter" data-level="14.6.5" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#deploy-the-page"><i class="fa fa-check"></i><b>14.6.5</b> Deploy the Page</a></li>
 </ul></li>
-<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-4"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
+<li class="chapter" data-level="14.7" data-path="making-your-own-website-with-postcards.html"><a href="making-your-own-website-with-postcards.html#references-5"><i class="fa fa-check"></i><b>14.7</b> References</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="final-r-session.html"><a href="final-r-session.html"><i class="fa fa-check"></i>Final R Session</a></li>
 </ul>