diff --git a/404.html b/404.html
index 07f02d3..2a85c16 100644
--- a/404.html
+++ b/404.html
@@ -324,8 +324,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 3b33b49..12b8074 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -346,7 +346,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index c840862..7852aa2 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -397,7 +397,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index fbb5d28..c53e0be 100644
--- a/aio.html
+++ b/aio.html
@@ -825,7 +825,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
-<p>Last updated on 2024-05-23 |
+<p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -946,11 +946,11 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 id="testing-for-empty-droplets">Testing for empty droplets<a class="anchor" aria-label="anchor" href="#testing-for-empty-droplets"></a>
 </h3>
 <p>A better approach is to test whether the expression profile for each
-cell barcode is significantly different from the ambient RNA pool <span class="citation">[@lun2019emptydrops]</span>. Any significant deviation
-indicates that the barcode corresponds to a cell-containing droplet.
-This allows us to discriminate between well-sequenced empty droplets and
-droplets derived from cells with little RNA, both of which would have
-similar total counts.</p>
+cell barcode is significantly different from the ambient RNA pool<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>. Any
+significant deviation indicates that the barcode corresponds to a
+cell-containing droplet. This allows us to discriminate between
+well-sequenced empty droplets and droplets derived from cells with
+little RNA, both of which would have similar total counts.</p>
 <p>We call cells at a false discovery rate (FDR) of 0.1%, meaning that
 no more than 0.1% of our called barcodes should be empty droplets on
 average.</p>
@@ -1005,7 +1005,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1042,8 +1042,8 @@ <h3 class="accordion-header" id="headingSpoiler1">
 <h3 id="choice-of-quality-control-metrics">Choice of quality-control metrics<a class="anchor" aria-label="anchor" href="#choice-of-quality-control-metrics"></a>
 </h3>
 <p>There are many possible ways to define a set of quality-control
-metrics, see for instance <span class="citation">@cole2019performance</span>. Here, we keep it simple
-and consider only:</p>
+metrics, see for instance <a href="reference.html#litref">Cole 2019</a>.
+Here, we keep it simple and consider only:</p>
 <ul>
 <li>the <em>library size</em>, defined as the total sum of counts across
 all relevant features for each cell;</li>
@@ -1299,11 +1299,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 often observed in single-cell RNA sequencing data. They typically arise
 from technical differences in cDNA capture or PCR amplification
 efficiency across cells, attributable to the difficulty of achieving
-consistent library preparation with minimal starting material <span class="citation">[@vallejos2017normalizing]</span>. Normalization aims
-to remove these differences such that they do not interfere with
-comparisons of the expression profiles between cells. The hope is that
-the observed heterogeneity or differential expression within the cell
-population are driven by biology and not technical biases.</p>
+consistent library preparation with minimal starting material<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a>.
+Normalization aims to remove these differences such that they do not
+interfere with comparisons of the expression profiles between cells. The
+hope is that the observed heterogeneity or differential expression
+within the cell population are driven by biology and not technical
+biases.</p>
 <p>We will mostly focus our attention on scaling normalization, which is
 the simplest and most commonly used class of normalization strategies.
 This involves dividing all counts for each cell by a cell-specific
@@ -1353,9 +1354,9 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 RNA-seq. However, these methods may underperform in single-cell data due
 to the dominance of low and zero counts. To overcome this, one solution
 is to <em>pool</em> counts from many cells to increase the size of the
-counts for accurate size factor estimation <span class="citation">[@l2016pooling]</span>. Pool-based size factors are
-then <em>deconvolved</em> into cell-based factors for normalization of
-each cell’s expression profile.</p>
+counts for accurate size factor estimation<a href="#fn3" class="footnote-ref" id="fnref3"><sup>3</sup></a>. Pool-based size
+factors are then <em>deconvolved</em> into cell-based factors for
+normalization of each cell’s expression profile.</p>
 <p>We use a pre-clustering step: cells in each cluster are normalized
 separately and the size factors are rescaled to be comparable across
 clusters. This avoids the assumption that most genes are non-DE across
@@ -1363,8 +1364,7 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 of clusters, which is a weaker assumption for highly heterogeneous
 populations.</p>
 <p>Note that while we focus on normalization by deconvolution here, many
-other methods have been proposed and lead to similar performance (see
-<span class="citation">@borella2022psinorm</span> for a comparative
+other methods have been proposed and lead to similar performance (see <a href="reference.html#litref">Borella 2022</a> for a comparative
 review).</p>
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1813,7 +1813,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1900,13 +1900,18 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width">
 <!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- --></section></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
+ -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr>
+<ol>
+<li id="fn1"><p><a href="reference.html#litref">Lun (2019)</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+<li id="fn2"><p><a href="reference.html#litref">Vallejos (2017)</a><a href="#fnref2" class="footnote-back">↩︎</a></p></li>
+<li id="fn3"><p><a href="reference.html#litref">Lun (2016)</a><a href="#fnref3" class="footnote-back">↩︎</a></p></li>
+</ol>
+</div></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
 <hr>
 <p>Last updated on 2024-05-23 |
         
@@ -5190,7 +5195,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 any links that you are not going to use. 
  --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
-<p>Last updated on 2024-05-23 |
+<p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -5268,9 +5273,8 @@ <h3 class="card-title">Objectives</h3>
 <p>To model the immune system across studies, we adopted a consistent
 immune cell-type ontology appropriate for lymphoid and non-lymphoid
 tissues. We applied a consensus cell labeling strategy between the
-Seurat blueprint and Monaco <span class="citation">[-@Monaco2019]</span>
-to minimize biases in immune cell classification from study-specific
-standards.</p>
+Seurat blueprint and Monaco<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a> to minimize biases in immune cell
+classification from study-specific standards.</p>
 <p><code>CuratedAtlasQueryR</code> supports data access and programmatic
 exploration of the harmonized atlas. Cells of interest can be selected
 based on ontology, tissue of origin, demographics, and disease. For
@@ -5853,7 +5857,12 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
  -->
-</section></section>
+</section><div class="footnotes footnotes-end-of-document">
+<hr>
+<ol>
+<li id="fn1"><p><a href="reference.html#litref">Monaco 2019</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+</ol>
+</div></section>
 </div>
     </main>
 </div>
@@ -5901,8 +5910,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 41d3efa..e4b04d1 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1560,7 +1560,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index 1b98575..d7d0113 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -180,7 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#dimensionality-reduction">Dimensionality Reduction</a></li>
 <li><a href="#doublet-identification">Doublet identification</a></li>
 <li><a href="#exercises">Exercises</a></li>
-<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
         
@@ -281,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory data analysis and quality control</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -399,11 +398,11 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="section level3">
 <h3 id="testing-for-empty-droplets">Testing for empty droplets<a class="anchor" aria-label="anchor" href="#testing-for-empty-droplets"></a></h3>
 <p>A better approach is to test whether the expression profile for each
-cell barcode is significantly different from the ambient RNA pool <span class="citation">[@lun2019emptydrops]</span>. Any significant deviation
-indicates that the barcode corresponds to a cell-containing droplet.
-This allows us to discriminate between well-sequenced empty droplets and
-droplets derived from cells with little RNA, both of which would have
-similar total counts.</p>
+cell barcode is significantly different from the ambient RNA pool<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>. Any
+significant deviation indicates that the barcode corresponds to a
+cell-containing droplet. This allows us to discriminate between
+well-sequenced empty droplets and droplets derived from cells with
+little RNA, both of which would have similar total counts.</p>
 <p>We call cells at a false discovery rate (FDR) of 0.1%, meaning that
 no more than 0.1% of our called barcodes should be empty droplets on
 average.</p>
@@ -458,7 +457,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -491,8 +490,8 @@ <h3 class="accordion-header" id="headingSpoiler1">
 <div class="section level3">
 <h3 id="choice-of-quality-control-metrics">Choice of quality-control metrics<a class="anchor" aria-label="anchor" href="#choice-of-quality-control-metrics"></a></h3>
 <p>There are many possible ways to define a set of quality-control
-metrics, see for instance <span class="citation">@cole2019performance</span>. Here, we keep it simple
-and consider only:</p>
+metrics, see for instance <a href="reference.html#litref">Cole 2019</a>.
+Here, we keep it simple and consider only:</p>
 <ul><li>the <em>library size</em>, defined as the total sum of counts across
 all relevant features for each cell;</li>
 <li>the number of expressed features in each cell, defined as the number
@@ -744,11 +743,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 often observed in single-cell RNA sequencing data. They typically arise
 from technical differences in cDNA capture or PCR amplification
 efficiency across cells, attributable to the difficulty of achieving
-consistent library preparation with minimal starting material <span class="citation">[@vallejos2017normalizing]</span>. Normalization aims
-to remove these differences such that they do not interfere with
-comparisons of the expression profiles between cells. The hope is that
-the observed heterogeneity or differential expression within the cell
-population are driven by biology and not technical biases.</p>
+consistent library preparation with minimal starting material<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a>.
+Normalization aims to remove these differences such that they do not
+interfere with comparisons of the expression profiles between cells. The
+hope is that the observed heterogeneity or differential expression
+within the cell population are driven by biology and not technical
+biases.</p>
 <p>We will mostly focus our attention on scaling normalization, which is
 the simplest and most commonly used class of normalization strategies.
 This involves dividing all counts for each cell by a cell-specific
@@ -797,9 +797,9 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 RNA-seq. However, these methods may underperform in single-cell data due
 to the dominance of low and zero counts. To overcome this, one solution
 is to <em>pool</em> counts from many cells to increase the size of the
-counts for accurate size factor estimation <span class="citation">[@l2016pooling]</span>. Pool-based size factors are
-then <em>deconvolved</em> into cell-based factors for normalization of
-each cell’s expression profile.</p>
+counts for accurate size factor estimation<a href="#fn3" class="footnote-ref" id="fnref3"><sup>3</sup></a>. Pool-based size
+factors are then <em>deconvolved</em> into cell-based factors for
+normalization of each cell’s expression profile.</p>
 <p>We use a pre-clustering step: cells in each cluster are normalized
 separately and the size factors are rescaled to be comparable across
 clusters. This avoids the assumption that most genes are non-DE across
@@ -807,8 +807,7 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 of clusters, which is a weaker assumption for highly heterogeneous
 populations.</p>
 <p>Note that while we focus on normalization by deconvolution here, many
-other methods have been proposed and lead to similar performance (see
-<span class="citation">@borella2022psinorm</span> for a comparative
+other methods have been proposed and lead to similar performance (see <a href="reference.html#litref">Borella 2022</a> for a comparative
 review).</p>
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1245,7 +1244,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1328,12 +1327,19 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </ul></div>
 </div>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width"><!-- 
+<!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- --></section></div> <!-- / div.lesson-content -->
+ -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr><ol><li id="fn1"><p><a href="reference.html#litref">Lun (2019)</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+<li id="fn2"><p><a href="reference.html#litref">Vallejos (2017)</a><a href="#fnref2" class="footnote-back">↩︎</a></p></li>
+<li id="fn3"><p><a href="reference.html#litref">Lun (2016)</a><a href="#fnref3" class="footnote-back">↩︎</a></p></li>
+</ol></div>
+
+
+
+      </div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="intro-sce.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="cell_type_annotation.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -1391,8 +1397,8 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
   "url": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/hca.html b/hca.html
index 556669b..d3ff49f 100644
--- a/hca.html
+++ b/hca.html
@@ -286,7 +286,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Accessing data from the Human Cell Atlas (HCA)</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -362,9 +362,8 @@ <h3 class="card-title">Objectives</h3>
 <p>To model the immune system across studies, we adopted a consistent
 immune cell-type ontology appropriate for lymphoid and non-lymphoid
 tissues. We applied a consensus cell labeling strategy between the
-Seurat blueprint and Monaco <span class="citation">[-@Monaco2019]</span>
-to minimize biases in immune cell classification from study-specific
-standards.</p>
+Seurat blueprint and Monaco<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a> to minimize biases in immune cell
+classification from study-specific standards.</p>
 <p><code>CuratedAtlasQueryR</code> supports data access and programmatic
 exploration of the harmonized atlas. Cells of interest can be selected
 based on ontology, tissue of origin, demographics, and disease. For
@@ -912,7 +911,13 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
  -->
-</section></div> <!-- / div.lesson-content -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr><ol><li id="fn1"><p><a href="reference.html#litref">Monaco 2019</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+</ol></div>
+
+
+
+      </div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="large_data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -970,8 +975,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index b11d044..04764df 100644
--- a/images.html
+++ b/images.html
@@ -430,8 +430,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index dc21d46..b913422 100644
--- a/index.html
+++ b/index.html
@@ -522,8 +522,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
   "url": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 61ef69f..c2bc3ef 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -364,8 +364,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index c6d51e1..8648e5e 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -324,8 +324,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 13ac6b5..0ac1166 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -348,7 +348,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index a63bbc9..a766520 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -399,7 +399,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 7e5f41c..f064f18 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -828,7 +828,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
-<p>Last updated on 2024-05-23 |
+<p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -950,11 +950,11 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 id="testing-for-empty-droplets">Testing for empty droplets<a class="anchor" aria-label="anchor" href="#testing-for-empty-droplets"></a>
 </h3>
 <p>A better approach is to test whether the expression profile for each
-cell barcode is significantly different from the ambient RNA pool <span class="citation">[@lun2019emptydrops]</span>. Any significant deviation
-indicates that the barcode corresponds to a cell-containing droplet.
-This allows us to discriminate between well-sequenced empty droplets and
-droplets derived from cells with little RNA, both of which would have
-similar total counts.</p>
+cell barcode is significantly different from the ambient RNA pool<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>. Any
+significant deviation indicates that the barcode corresponds to a
+cell-containing droplet. This allows us to discriminate between
+well-sequenced empty droplets and droplets derived from cells with
+little RNA, both of which would have similar total counts.</p>
 <p>We call cells at a false discovery rate (FDR) of 0.1%, meaning that
 no more than 0.1% of our called barcodes should be empty droplets on
 average.</p>
@@ -1009,7 +1009,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1046,8 +1046,8 @@ <h3 class="accordion-header" id="headingSpoiler1">
 <h3 id="choice-of-quality-control-metrics">Choice of quality-control metrics<a class="anchor" aria-label="anchor" href="#choice-of-quality-control-metrics"></a>
 </h3>
 <p>There are many possible ways to define a set of quality-control
-metrics, see for instance <span class="citation">@cole2019performance</span>. Here, we keep it simple
-and consider only:</p>
+metrics, see for instance <a href="reference.html#litref">Cole 2019</a>.
+Here, we keep it simple and consider only:</p>
 <ul>
 <li>the <em>library size</em>, defined as the total sum of counts across
 all relevant features for each cell;</li>
@@ -1303,11 +1303,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 often observed in single-cell RNA sequencing data. They typically arise
 from technical differences in cDNA capture or PCR amplification
 efficiency across cells, attributable to the difficulty of achieving
-consistent library preparation with minimal starting material <span class="citation">[@vallejos2017normalizing]</span>. Normalization aims
-to remove these differences such that they do not interfere with
-comparisons of the expression profiles between cells. The hope is that
-the observed heterogeneity or differential expression within the cell
-population are driven by biology and not technical biases.</p>
+consistent library preparation with minimal starting material<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a>.
+Normalization aims to remove these differences such that they do not
+interfere with comparisons of the expression profiles between cells. The
+hope is that the observed heterogeneity or differential expression
+within the cell population are driven by biology and not technical
+biases.</p>
 <p>We will mostly focus our attention on scaling normalization, which is
 the simplest and most commonly used class of normalization strategies.
 This involves dividing all counts for each cell by a cell-specific
@@ -1357,9 +1358,9 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 RNA-seq. However, these methods may underperform in single-cell data due
 to the dominance of low and zero counts. To overcome this, one solution
 is to <em>pool</em> counts from many cells to increase the size of the
-counts for accurate size factor estimation <span class="citation">[@l2016pooling]</span>. Pool-based size factors are
-then <em>deconvolved</em> into cell-based factors for normalization of
-each cell’s expression profile.</p>
+counts for accurate size factor estimation<a href="#fn3" class="footnote-ref" id="fnref3"><sup>3</sup></a>. Pool-based size
+factors are then <em>deconvolved</em> into cell-based factors for
+normalization of each cell’s expression profile.</p>
 <p>We use a pre-clustering step: cells in each cluster are normalized
 separately and the size factors are rescaled to be comparable across
 clusters. This avoids the assumption that most genes are non-DE across
@@ -1367,8 +1368,7 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 of clusters, which is a weaker assumption for highly heterogeneous
 populations.</p>
 <p>Note that while we focus on normalization by deconvolution here, many
-other methods have been proposed and lead to similar performance (see
-<span class="citation">@borella2022psinorm</span> for a comparative
+other methods have been proposed and lead to similar performance (see <a href="reference.html#litref">Borella 2022</a> for a comparative
 review).</p>
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1817,7 +1817,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1904,13 +1904,18 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </div>
 </div>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width">
 <!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- --></section></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
+ -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr>
+<ol>
+<li id="fn1"><p><a href="reference.html#litref">Lun (2019)</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+<li id="fn2"><p><a href="reference.html#litref">Vallejos (2017)</a><a href="#fnref2" class="footnote-back">↩︎</a></p></li>
+<li id="fn3"><p><a href="reference.html#litref">Lun (2016)</a><a href="#fnref3" class="footnote-back">↩︎</a></p></li>
+</ol>
+</div></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
 <hr>
 <p>Last updated on 2024-05-23 |
         
@@ -5197,7 +5202,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 any links that you are not going to use. 
  --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
-<p>Last updated on 2024-05-23 |
+<p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -5276,9 +5281,8 @@ <h3 class="card-title">Objectives</h3>
 <p>To model the immune system across studies, we adopted a consistent
 immune cell-type ontology appropriate for lymphoid and non-lymphoid
 tissues. We applied a consensus cell labeling strategy between the
-Seurat blueprint and Monaco <span class="citation">[-@Monaco2019]</span>
-to minimize biases in immune cell classification from study-specific
-standards.</p>
+Seurat blueprint and Monaco<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a> to minimize biases in immune cell
+classification from study-specific standards.</p>
 <p><code>CuratedAtlasQueryR</code> supports data access and programmatic
 exploration of the harmonized atlas. Cells of interest can be selected
 based on ontology, tissue of origin, demographics, and disease. For
@@ -5861,7 +5865,12 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
  -->
-</section></section>
+</section><div class="footnotes footnotes-end-of-document">
+<hr>
+<ol>
+<li id="fn1"><p><a href="reference.html#litref">Monaco 2019</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+</ol>
+</div></section>
 </div>
     </main>
 </div>
@@ -5909,8 +5918,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 98ac78d..bad4336 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -1562,7 +1562,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 173818b..bb5ea0d 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -180,7 +180,6 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#dimensionality-reduction">Dimensionality Reduction</a></li>
 <li><a href="#doublet-identification">Doublet identification</a></li>
 <li><a href="#exercises">Exercises</a></li>
-<li><a href="#references">References</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
         
@@ -281,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory data analysis and quality control</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -401,11 +400,11 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="section level3">
 <h3 id="testing-for-empty-droplets">Testing for empty droplets<a class="anchor" aria-label="anchor" href="#testing-for-empty-droplets"></a></h3>
 <p>A better approach is to test whether the expression profile for each
-cell barcode is significantly different from the ambient RNA pool <span class="citation">[@lun2019emptydrops]</span>. Any significant deviation
-indicates that the barcode corresponds to a cell-containing droplet.
-This allows us to discriminate between well-sequenced empty droplets and
-droplets derived from cells with little RNA, both of which would have
-similar total counts.</p>
+cell barcode is significantly different from the ambient RNA pool<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>. Any
+significant deviation indicates that the barcode corresponds to a
+cell-containing droplet. This allows us to discriminate between
+well-sequenced empty droplets and droplets derived from cells with
+little RNA, both of which would have similar total counts.</p>
 <p>We call cells at a false discovery rate (FDR) of 0.1%, meaning that
 no more than 0.1% of our called barcodes should be empty droplets on
 average.</p>
@@ -460,7 +459,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -493,8 +492,8 @@ <h3 class="accordion-header" id="headingSpoiler1">
 <div class="section level3">
 <h3 id="choice-of-quality-control-metrics">Choice of quality-control metrics<a class="anchor" aria-label="anchor" href="#choice-of-quality-control-metrics"></a></h3>
 <p>There are many possible ways to define a set of quality-control
-metrics, see for instance <span class="citation">@cole2019performance</span>. Here, we keep it simple
-and consider only:</p>
+metrics, see for instance <a href="reference.html#litref">Cole 2019</a>.
+Here, we keep it simple and consider only:</p>
 <ul><li>the <em>library size</em>, defined as the total sum of counts across
 all relevant features for each cell;</li>
 <li>the number of expressed features in each cell, defined as the number
@@ -746,11 +745,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 often observed in single-cell RNA sequencing data. They typically arise
 from technical differences in cDNA capture or PCR amplification
 efficiency across cells, attributable to the difficulty of achieving
-consistent library preparation with minimal starting material <span class="citation">[@vallejos2017normalizing]</span>. Normalization aims
-to remove these differences such that they do not interfere with
-comparisons of the expression profiles between cells. The hope is that
-the observed heterogeneity or differential expression within the cell
-population are driven by biology and not technical biases.</p>
+consistent library preparation with minimal starting material<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a>.
+Normalization aims to remove these differences such that they do not
+interfere with comparisons of the expression profiles between cells. The
+hope is that the observed heterogeneity or differential expression
+within the cell population are driven by biology and not technical
+biases.</p>
 <p>We will mostly focus our attention on scaling normalization, which is
 the simplest and most commonly used class of normalization strategies.
 This involves dividing all counts for each cell by a cell-specific
@@ -799,9 +799,9 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 RNA-seq. However, these methods may underperform in single-cell data due
 to the dominance of low and zero counts. To overcome this, one solution
 is to <em>pool</em> counts from many cells to increase the size of the
-counts for accurate size factor estimation <span class="citation">[@l2016pooling]</span>. Pool-based size factors are
-then <em>deconvolved</em> into cell-based factors for normalization of
-each cell’s expression profile.</p>
+counts for accurate size factor estimation<a href="#fn3" class="footnote-ref" id="fnref3"><sup>3</sup></a>. Pool-based size
+factors are then <em>deconvolved</em> into cell-based factors for
+normalization of each cell’s expression profile.</p>
 <p>We use a pre-clustering step: cells in each cluster are normalized
 separately and the size factors are rescaled to be comparable across
 clusters. This avoids the assumption that most genes are non-DE across
@@ -809,8 +809,7 @@ <h3 id="normalization-by-deconvolution">Normalization by deconvolution<a class="
 of clusters, which is a weaker assumption for highly heterogeneous
 populations.</p>
 <p>Note that while we focus on normalization by deconvolution here, many
-other methods have been proposed and lead to similar performance (see
-<span class="citation">@borella2022psinorm</span> for a comparative
+other methods have been proposed and lead to similar performance (see <a href="reference.html#litref">Borella 2022</a> for a comparative
 review).</p>
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1247,7 +1246,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1330,12 +1329,19 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </ul></div>
 </div>
 </div>
-</section><section id="references"><h2 class="section-heading">References<a class="anchor" aria-label="anchor" href="#references"></a>
-</h2>
-<hr class="half-width"><!-- 
+<!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- --></section></div> <!-- / div.lesson-content -->
+ -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr><ol><li id="fn1"><p><a href="reference.html#litref">Lun (2019)</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+<li id="fn2"><p><a href="reference.html#litref">Vallejos (2017)</a><a href="#fnref2" class="footnote-back">↩︎</a></p></li>
+<li id="fn3"><p><a href="reference.html#litref">Lun (2016)</a><a href="#fnref3" class="footnote-back">↩︎</a></p></li>
+</ol></div>
+
+
+
+      </div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/intro-sce.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="../instructor/cell_type_annotation.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -1393,8 +1399,8 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
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diff --git a/instructor/hca.html b/instructor/hca.html
index 3814e3b..9ffc778 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -286,7 +286,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Accessing data from the Human Cell Atlas (HCA)</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -364,9 +364,8 @@ <h3 class="card-title">Objectives</h3>
 <p>To model the immune system across studies, we adopted a consistent
 immune cell-type ontology appropriate for lymphoid and non-lymphoid
 tissues. We applied a consensus cell labeling strategy between the
-Seurat blueprint and Monaco <span class="citation">[-@Monaco2019]</span>
-to minimize biases in immune cell classification from study-specific
-standards.</p>
+Seurat blueprint and Monaco<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a> to minimize biases in immune cell
+classification from study-specific standards.</p>
 <p><code>CuratedAtlasQueryR</code> supports data access and programmatic
 exploration of the harmonized atlas. Cells of interest can be selected
 based on ontology, tissue of origin, demographics, and disease. For
@@ -914,7 +913,13 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
  -->
-</section></div> <!-- / div.lesson-content -->
+</section><div class="footnotes footnotes-end-of-document">
+<hr><ol><li id="fn1"><p><a href="reference.html#litref">Monaco 2019</a><a href="#fnref1" class="footnote-back">↩︎</a></p></li>
+</ol></div>
+
+
+
+      </div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/large_data.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="../instructor/index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -972,8 +977,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
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diff --git a/instructor/images.html b/instructor/images.html
index a36600c..ca37da6 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -432,8 +432,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
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diff --git a/instructor/index.html b/instructor/index.html
index cc26278..33c0e76 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -606,8 +606,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 9b0f9f4..ca840bd 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -372,8 +372,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index b9ccccc..1ff021e 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -837,7 +837,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index d151975..55f5604 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -482,8 +482,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "dateCreated": "2024-01-10",
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-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
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diff --git a/instructor/large_data.html b/instructor/large_data.html
index 13d8ce3..437f24e 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -1346,7 +1346,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
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diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index aa379eb..d3d2925 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -1345,7 +1345,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index a938927..b8208a7 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -299,8 +299,8 @@ <h1>Learner Profiles</h1>
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   "dateCreated": "2024-01-10",
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 }
 
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diff --git a/instructor/reference.html b/instructor/reference.html
index 69260d3..8f03239 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -275,14 +275,34 @@ <h1>Reference</h1>
         </div>
 
         
-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
+<section id="litref"><h2 class="section-heading">Literature Reference<a class="anchor" aria-label="anchor" href="#litref"></a>
 </h2>
-<hr class="half-width"><p>This is a placeholder file. Please add content here.</p>
-<!-- 
+<hr class="half-width"><ol style="list-style-type: decimal"><li>Borella, Matteo, Graziano Martello, Davide Risso, and Chiara
+Romualdi. “PsiNorm: A Scalable Normalization for Single-Cell RNA-Seq
+Data.” Bioinformatics 38, no. 1 (2022): 164–72.</li>
+<li>Cole, Michael B, Davide Risso, Allon Wagner, David DeTomaso, John
+Ngai, Elizabeth Purdom, Sandrine Dudoit, and Nir Yosef. “Performance
+Assessment and Selection of Normalization Procedures for Single-Cell
+RNA-Seq.” Cell Systems 8, no. 4 (2019): 315–28.</li>
+<li>Lun, Aaron T, Karsten Bach, and John C Marioni. “Pooling across
+Cells to Normalize Single-Cell RNA Sequencing Data with Many Zero
+Counts.” Genome Biology 17, no. 1 (2016): 1–14.</li>
+<li>Lun, Aaron TL, Samantha Riesenfeld, Tallulah Andrews, Tomas Gomes,
+John C Marioni, and others. “EmptyDrops: Distinguishing Cells from Empty
+Droplets in Droplet-Based Single-Cell RNA Sequencing Data.” Genome
+Biology 20, no. 1 (2019): 1–9.</li>
+<li>Monaco, Gianni, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang,
+Christophe Carré, Nicolas Burdin, et al. “RNA-Seq Signatures Normalized
+by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell
+Types.” Cell Rep. 26, no. 6 (February 2019): 1627-1640.e7.</li>
+<li>Vallejos, Catalina A, Davide Risso, Antonio Scialdone, Sandrine
+Dudoit, and John C Marioni. “Normalizing Single-Cell RNA Sequencing
+Data: Challenges and Opportunities.” Nature Methods 14, no. 6 (2017):
+565–71.</li>
+</ol><!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- -->
-</section></div> <!-- / div.lesson-content -->
+ --></section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="../instructor/index.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="../instructor/index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -340,8 +360,8 @@ <h1>Reference</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
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diff --git a/intro-sce.html b/intro-sce.html
index b19c42f..26ce334 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -835,7 +835,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index aed3f44..d6d570f 100644
--- a/key-points.html
+++ b/key-points.html
@@ -480,8 +480,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index f4d0545..0b0c685 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1344,7 +1344,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index 9bcb5a9..288fc28 100644
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diff --git a/multi-sample.html b/multi-sample.html
index 365e4e2..a775b10 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -1343,7 +1343,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 850bfbb..89a4672 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-28T00:35Z
+last_built: 2024-05-29T00:20Z
 
diff --git a/profiles.html b/profiles.html
index b76e213..ad72117 100644
--- a/profiles.html
+++ b/profiles.html
@@ -299,8 +299,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-28",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 3ed0ef0..b29b39b 100644
--- a/reference.html
+++ b/reference.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-05-23 |
+        <p>Last updated on 2024-05-29 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -273,14 +273,34 @@ <h1>Reference</h1>
         </div>
 
         
-<section id="glossary"><h2 class="section-heading">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a>
+<section id="litref"><h2 class="section-heading">Literature Reference<a class="anchor" aria-label="anchor" href="#litref"></a>
 </h2>
-<hr class="half-width"><p>This is a placeholder file. Please add content here.</p>
-<!-- 
+<hr class="half-width"><ol style="list-style-type: decimal"><li>Borella, Matteo, Graziano Martello, Davide Risso, and Chiara
+Romualdi. “PsiNorm: A Scalable Normalization for Single-Cell RNA-Seq
+Data.” Bioinformatics 38, no. 1 (2022): 164–72.</li>
+<li>Cole, Michael B, Davide Risso, Allon Wagner, David DeTomaso, John
+Ngai, Elizabeth Purdom, Sandrine Dudoit, and Nir Yosef. “Performance
+Assessment and Selection of Normalization Procedures for Single-Cell
+RNA-Seq.” Cell Systems 8, no. 4 (2019): 315–28.</li>
+<li>Lun, Aaron T, Karsten Bach, and John C Marioni. “Pooling across
+Cells to Normalize Single-Cell RNA Sequencing Data with Many Zero
+Counts.” Genome Biology 17, no. 1 (2016): 1–14.</li>
+<li>Lun, Aaron TL, Samantha Riesenfeld, Tallulah Andrews, Tomas Gomes,
+John C Marioni, and others. “EmptyDrops: Distinguishing Cells from Empty
+Droplets in Droplet-Based Single-Cell RNA Sequencing Data.” Genome
+Biology 20, no. 1 (2019): 1–9.</li>
+<li>Monaco, Gianni, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang,
+Christophe Carré, Nicolas Burdin, et al. “RNA-Seq Signatures Normalized
+by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell
+Types.” Cell Rep. 26, no. 6 (February 2019): 1627-1640.e7.</li>
+<li>Vallejos, Catalina A, Davide Risso, Antonio Scialdone, Sandrine
+Dudoit, and John C Marioni. “Normalizing Single-Cell RNA Sequencing
+Data: Challenges and Opportunities.” Nature Methods 14, no. 6 (2017):
+565–71.</li>
+</ol><!-- 
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use. 
- -->
-</section></div> <!-- / div.lesson-content -->
+ --></section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
         <a class="chapter-link" href="index.html"><i aria-hidden="true" class="small-arrow" data-feather="arrow-left"></i>Previous</a>
         <a class="chapter-link float-end" href="index.html">Next<i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i></a>
@@ -338,8 +358,8 @@ <h1>Reference</h1>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
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-  "dateModified": "2024-05-23",
-  "datePublished": "2024-05-28"
+  "dateModified": "2024-05-29",
+  "datePublished": "2024-05-29"
 }
 
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