From 921d118744f74cfdfd50c5b04281635c4bef7c32 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 4 Oct 2024 17:50:05 +0000
Subject: [PATCH] site deploy

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Source  : 8b3e092f207a6403668e8b9fcd3371d14fa39bfe
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-10-04 17:48:36 +0000
Message : markdown source builds

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Source  : 62aa52b0bac743acad8ad048126e8634bf9e43ca
Branch  : main
Author  : Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Time    : 2024-10-04 17:07:47 +0000
Message : Merge pull request #53 from ccb-hms/eval_meta_ex

eval exercises
---
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 hca.html                                      |  98 +++++++++--
 index.html                                    |  10 +-
 instructor/aio.html                           | 153 +++++++++++++-----
 instructor/hca.html                           |  98 +++++++++--
 instructor/index.html                         |  10 +-
 instructor/large_data.html                    |  41 +++--
 instructor/multi-sample.html                  |  16 +-
 large_data.html                               |  41 +++--
 md5sum.txt                                    |   2 +-
 multi-sample.html                             |  16 +-
 pkgdown.yml                                   |   2 +-
 21 files changed, 466 insertions(+), 174 deletions(-)
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diff --git a/aio.html b/aio.html
index a7585f8..b1902cf 100644
--- a/aio.html
+++ b/aio.html
@@ -4141,7 +4141,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -4206,7 +4206,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -4659,7 +4659,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -4985,7 +4985,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -4999,7 +4999,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5034,7 +5034,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -5049,7 +5049,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5132,7 +5132,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5627,7 +5627,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -5701,21 +5701,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
-   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
-   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
-   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
-   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
-   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
-   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
-   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
+   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
+   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
+   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
+   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
+   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
+   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -5860,7 +5859,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -6271,7 +6270,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -6285,7 +6284,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6364,7 +6363,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -6377,7 +6376,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6451,7 +6450,7 @@ <h3 class="callout-title">Key Points</h3>
 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 2024-10-03 |
+<p>Last updated on 2024-10-04 |
 
         <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">
@@ -6922,7 +6921,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6932,6 +6931,24 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -6955,9 +6972,9 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -6966,6 +6983,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu">head</span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 3
+  tissue           cell_type                              n
+  &lt;chr&gt;            &lt;chr&gt;                              &lt;int&gt;
+1 cortex of kidney epithelial cell of proximal tubule 29986</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -6988,20 +7013,68 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
+<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb29">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue_harmonised</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 19 × 2
+   tissue_harmonised     n
+   &lt;chr&gt;             &lt;int&gt;
+ 1 kidney            68851
+ 2 lung              25737
+ 3 blood              4248
+ 4 bone               4113
+ 5 heart              1454
+ 6 lymph node         1210
+ 7 prostate           1156
+ 8 intestine large     816
+ 9 liver               793
+10 thymus              753
+11 intestine small     530
+12 eye                 437
+13 intestine           360
+14 esophagus           334
+15 nose                290
+16 vasculature         143
+17 brain                97
+18 adrenal gland        20
+19 axilla               13</code></pre>
+</div>
 <p>For example you can see that <code>tissue_harmonised</code> merges
 the <code>cortex of kidney</code> and <code>kidney</code> groups in
 <code>tissue</code>.</p>
@@ -7032,9 +7105,9 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
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diff --git a/hca.html b/hca.html
index b01a18e..f53511d 100644
--- a/hca.html
+++ b/hca.html
@@ -319,7 +319,7 @@ <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 2024-10-03 |
+        <p>Last updated on 2024-10-04 |
 
         <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>
 
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -768,6 +768,24 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -791,9 +809,9 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -802,6 +820,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu">head</span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 3
+  tissue           cell_type                              n
+  &lt;chr&gt;            &lt;chr&gt;                              &lt;int&gt;
+1 cortex of kidney epithelial cell of proximal tubule 29986</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -824,20 +850,68 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
+<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb29">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue_harmonised</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 19 × 2
+   tissue_harmonised     n
+   &lt;chr&gt;             &lt;int&gt;
+ 1 kidney            68851
+ 2 lung              25737
+ 3 blood              4248
+ 4 bone               4113
+ 5 heart              1454
+ 6 lymph node         1210
+ 7 prostate           1156
+ 8 intestine large     816
+ 9 liver               793
+10 thymus              753
+11 intestine small     530
+12 eye                 437
+13 intestine           360
+14 esophagus           334
+15 nose                290
+16 vasculature         143
+17 brain                97
+18 adrenal gland        20
+19 axilla               13</code></pre>
+</div>
 <p>For example you can see that <code>tissue_harmonised</code> merges
 the <code>cortex of kidney</code> and <code>kidney</code> groups in
 <code>tissue</code>.</p>
@@ -868,9 +942,9 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -989,7 +1063,7 @@ <h3 class="callout-title">Key Points</h3>
   "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": "2024-10-03",
+  "dateModified": "2024-10-04",
   "datePublished": "2024-10-04"
 }
 
diff --git a/index.html b/index.html
index 9d519b2..4755282 100644
--- a/index.html
+++ b/index.html
@@ -372,7 +372,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -398,7 +398,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</li>
@@ -429,7 +429,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -453,7 +453,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
 <li>Select the <code>.pkg</code> file for the latest R version</li>
@@ -486,7 +486,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/aio.html b/instructor/aio.html
index 8120207..c13b2fd 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -4147,7 +4147,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -4212,7 +4212,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -4665,7 +4665,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -4991,7 +4991,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -5005,7 +5005,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5040,7 +5040,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -5055,7 +5055,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5138,7 +5138,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5634,7 +5634,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -5708,21 +5708,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
-   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
-   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
-   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
-   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
-   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
-   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
-   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
+   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
+   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
+   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
+   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
+   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
+   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -5867,7 +5866,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -6278,7 +6277,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -6292,7 +6291,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6371,7 +6370,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -6384,7 +6383,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
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@@ -6458,7 +6457,7 @@ <h3 class="callout-title">Key Points</h3>
 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 2024-10-03 |
+<p>Last updated on 2024-10-04 |
 
         <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>
@@ -6930,7 +6929,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6940,6 +6939,24 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -6963,9 +6980,9 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -6974,6 +6991,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu">head</span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 3
+  tissue           cell_type                              n
+  &lt;chr&gt;            &lt;chr&gt;                              &lt;int&gt;
+1 cortex of kidney epithelial cell of proximal tubule 29986</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -6996,20 +7021,68 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
+<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb29">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue_harmonised</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 19 × 2
+   tissue_harmonised     n
+   &lt;chr&gt;             &lt;int&gt;
+ 1 kidney            68851
+ 2 lung              25737
+ 3 blood              4248
+ 4 bone               4113
+ 5 heart              1454
+ 6 lymph node         1210
+ 7 prostate           1156
+ 8 intestine large     816
+ 9 liver               793
+10 thymus              753
+11 intestine small     530
+12 eye                 437
+13 intestine           360
+14 esophagus           334
+15 nose                290
+16 vasculature         143
+17 brain                97
+18 adrenal gland        20
+19 axilla               13</code></pre>
+</div>
 <p>For example you can see that <code>tissue_harmonised</code> merges
 the <code>cortex of kidney</code> and <code>kidney</code> groups in
 <code>tissue</code>.</p>
@@ -7040,9 +7113,9 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
diff --git a/instructor/hca.html b/instructor/hca.html
index f95afb1..baf6094 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -319,7 +319,7 @@ <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 2024-10-03 |
+        <p>Last updated on 2024-10-04 |
 
         <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>
 
@@ -760,7 +760,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -770,6 +770,24 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -793,9 +811,9 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb24">
+<div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -804,6 +822,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
 <span>    <span class="fu">head</span><span class="op">(</span>n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 1 × 3
+  tissue           cell_type                              n
+  &lt;chr&gt;            &lt;chr&gt;                              &lt;int&gt;
+1 cortex of kidney epithelial cell of proximal tubule 29986</code></pre>
+</div>
 </div>
 </div>
 </div>
@@ -826,20 +852,68 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue</span><span class="op">)</span> <span class="op">|&gt;</span></span>
-<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span>
-<span></span>
-<span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
+<span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
+</div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 33 × 2
+   tissue                          n
+   &lt;chr&gt;                       &lt;int&gt;
+ 1 cortex of kidney            36940
+ 2 kidney                      23549
+ 3 lung parenchyma             16719
+ 4 renal medulla                7729
+ 5 respiratory airway           7153
+ 6 blood                        4248
+ 7 bone marrow                  4113
+ 8 heart left ventricle         1454
+ 9 transition zone of prostate  1140
+10 lung                         1137
+# ℹ 23 more rows</code></pre>
+</div>
+<div class="codewrapper sourceCode" id="cb29">
+<h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">count</span><span class="op">(</span><span class="va">tissue_harmonised</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">arrange</span><span class="op">(</span><span class="op">-</span><span class="va">n</span><span class="op">)</span></span></code></pre>
 </div>
+<div class="codewrapper">
+<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
+</h3>
+<pre class="output" tabindex="0"><code># A tibble: 19 × 2
+   tissue_harmonised     n
+   &lt;chr&gt;             &lt;int&gt;
+ 1 kidney            68851
+ 2 lung              25737
+ 3 blood              4248
+ 4 bone               4113
+ 5 heart              1454
+ 6 lymph node         1210
+ 7 prostate           1156
+ 8 intestine large     816
+ 9 liver               793
+10 thymus              753
+11 intestine small     530
+12 eye                 437
+13 intestine           360
+14 esophagus           334
+15 nose                290
+16 vasculature         143
+17 brain                97
+18 adrenal gland        20
+19 axilla               13</code></pre>
+</div>
 <p>For example you can see that <code>tissue_harmonised</code> merges
 the <code>cortex of kidney</code> and <code>kidney</code> groups in
 <code>tissue</code>.</p>
@@ -870,9 +944,9 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
-<div class="codewrapper sourceCode" id="cb26">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -991,7 +1065,7 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-03",
+  "dateModified": "2024-10-04",
   "datePublished": "2024-10-04"
 }
 
diff --git a/instructor/index.html b/instructor/index.html
index 8767059..5c49738 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -457,7 +457,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -483,7 +483,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</li>
@@ -514,7 +514,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
 version is available, quit RStudio, and download the latest version for
@@ -538,7 +538,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
 <li>Select the <code>.pkg</code> file for the latest R version</li>
@@ -571,7 +571,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 23af1c4..caad6b4 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -748,7 +748,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -819,21 +819,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
-   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
-   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
-   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
-   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
-   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
-   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
-   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
+   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
+   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
+   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
+   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
+   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
+   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -977,7 +976,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1380,7 +1379,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1394,7 +1393,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1473,7 +1472,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1486,7 +1485,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 41b3eca..92d94d5 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -545,7 +545,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -608,7 +608,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1057,7 +1057,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1374,7 +1374,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1388,7 +1388,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
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@@ -1423,7 +1423,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1438,7 +1438,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1521,7 +1521,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/large_data.html b/large_data.html
index 2713a39..873987d 100644
--- a/large_data.html
+++ b/large_data.html
@@ -746,7 +746,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -817,21 +817,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   88   0   0   0   0   0   0   2   0   0   0   1   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   0   0   0   0   0   0   0   2   0   0   0
-   4    0   0   0 198   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0  71   0   0   0   1   0   3 322   0   0   0
-   6    0   0   0   0   0 210   0   0   0   0   0   0   0   0   0
-   7    0   0   0   0   0   0 245   0   1   0   0   0   0   0   0
-   8    0   0   0   0  95   0   0   0   0   0   0   0   0   0   0
-   9    1   0   0   0   0   0   0 106   0   0   0   1   0   0   0
-   10   0   0   0   0   0   0   0   0 112   0  10   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0 153   0   0   0   0   0
-   12   0   0   0   0   8   0   0   0   0   0 195   1   0   0   0
-   13   0   0   0   0   0   0   0   0   1   0   0   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  56   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   1   90   0   0   0   1   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
+   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0  56
+   5    0   0   0   0 392   0   0   1   0   1   0   0   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
+   7    0   0   0   0   0 245   0   0   0   1   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
+   9    1   0   0   0   2   0   0   0 106   0   0   0   0   0   0
+   10   0   0   0   0   0   0   0   0   0 105   0   0   0   0   0
+   11   0   0   0   0   0   0   1   0   0   5 147   0   0   0   0
+   12   0   0   0   0   1   0   0   0   0  23   0 199   0   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0</code></pre>
 </div>
 <p>The similarity of the two clusterings can be quantified by
 calculating the pairwise Rand index:</p>
@@ -975,7 +974,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1378,7 +1377,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1392,7 +1391,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb50">
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@@ -1471,7 +1470,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
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 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1484,7 +1483,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/md5sum.txt b/md5sum.txt
index 138fdf2..ca19511 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -9,7 +9,7 @@
 "episodes/cell_type_annotation.Rmd" "8fab6e0cbb60d6fe6a67a0004c5ce5ab" "site/built/cell_type_annotation.md" "2024-10-02"
 "episodes/multi-sample.Rmd" "6d47bd1941b7a83000873da8d836fba0" "site/built/multi-sample.md" "2024-10-04"
 "episodes/large_data.Rmd" "ba9660bc24664972f540bbe5fdc34d08" "site/built/large_data.md" "2024-10-04"
-"episodes/hca.Rmd" "247c19cda5e903d2eb1a5dd547d95506" "site/built/hca.md" "2024-10-03"
+"episodes/hca.Rmd" "1577de2f4a851c7e99e3a8459230d6f1" "site/built/hca.md" "2024-10-04"
 "instructors/instructor-notes.md" "205339793f625a1844a768dea8e4a9c8" "site/built/instructor-notes.md" "2024-09-24"
 "learners/reference.md" "40fc1d0be2412d2d9d434a5bc84e4de8" "site/built/reference.md" "2024-09-24"
 "learners/setup.md" "25772142a26fe3c0cebbe650f5683269" "site/built/setup.md" "2024-09-24"
diff --git a/multi-sample.html b/multi-sample.html
index fe986ce..a642ecf 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -543,7 +543,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -606,7 +606,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1055,7 +1055,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1372,7 +1372,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
 <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1386,7 +1386,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1421,7 +1421,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1436,7 +1436,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1519,7 +1519,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
diff --git a/pkgdown.yml b/pkgdown.yml
index eb7fc54..d9a51ae 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-04T17:44Z
+last_built: 2024-10-04T17:49Z