From fe4412686f7208b42fc268f0caa60e52991e93a5 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Mon, 30 Sep 2024 15:44:56 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : c0d42dd11410842bfeda4c62266b0f4f3138e905
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-09-30 15:43:53 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : cd3de4f013a58e22018f9d23d34f55da626a90f0
Branch  : main
Author  : Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Time    : 2024-09-30 15:12:56 +0000
Message : Merge pull request #45 from ccb-hms/hca_refresh

hca_refresh question titles
---
 aio.html                                      | 104 +++++++++---------
 ...-12_ff65ff8596c60eb7d0bdd5aeedfe9718.RData | Bin 0 -> 2850 bytes
 ...nk-12_ff65ff8596c60eb7d0bdd5aeedfe9718.rdb | Bin 0 -> 25211 bytes
 ...nk-12_ff65ff8596c60eb7d0bdd5aeedfe9718.rdx | Bin 0 -> 152 bytes
 ...-19_b12335fcd30dae61f9fefec6176876c8.RData | Bin 0 -> 2773 bytes
 ...nk-19_b12335fcd30dae61f9fefec6176876c8.rdb |   0
 ...nk-19_b12335fcd30dae61f9fefec6176876c8.rdx | Bin 0 -> 125 bytes
 ...-21_81720bcf9caf24fb5eaa8c1c7e296ee8.RData | Bin 0 -> 3162 bytes
 ...nk-21_81720bcf9caf24fb5eaa8c1c7e296ee8.rdb |   0
 ...nk-21_81720bcf9caf24fb5eaa8c1c7e296ee8.rdx | Bin 0 -> 125 bytes
 cell_type_annotation.html                     |  20 ++--
 hca.html                                      |  62 ++++++-----
 instructor/aio.html                           | 104 +++++++++---------
 instructor/cell_type_annotation.html          |  20 ++--
 instructor/hca.html                           |  62 ++++++-----
 instructor/intro-sce.html                     |  12 +-
 instructor/multi-sample.html                  |  14 +--
 intro-sce.html                                |  12 +-
 md5sum.txt                                    |   2 +-
 multi-sample.html                             |  14 +--
 pkgdown.yml                                   |   2 +-
 21 files changed, 226 insertions(+), 202 deletions(-)
 create mode 100644 cache/unnamed-chunk-12_ff65ff8596c60eb7d0bdd5aeedfe9718.RData
 create mode 100644 cache/unnamed-chunk-12_ff65ff8596c60eb7d0bdd5aeedfe9718.rdb
 create mode 100644 cache/unnamed-chunk-12_ff65ff8596c60eb7d0bdd5aeedfe9718.rdx
 create mode 100644 cache/unnamed-chunk-19_b12335fcd30dae61f9fefec6176876c8.RData
 create mode 100644 cache/unnamed-chunk-19_b12335fcd30dae61f9fefec6176876c8.rdb
 create mode 100644 cache/unnamed-chunk-19_b12335fcd30dae61f9fefec6176876c8.rdx
 create mode 100644 cache/unnamed-chunk-21_81720bcf9caf24fb5eaa8c1c7e296ee8.RData
 create mode 100644 cache/unnamed-chunk-21_81720bcf9caf24fb5eaa8c1c7e296ee8.rdb
 create mode 100644 cache/unnamed-chunk-21_81720bcf9caf24fb5eaa8c1c7e296ee8.rdx

diff --git a/aio.html b/aio.html
index 51b8bf2..814e28d 100644
--- a/aio.html
+++ b/aio.html
@@ -590,7 +590,7 @@ <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" 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">
 <p>Here we assign the sixth sample to <code>sce6</code>:</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -735,7 +735,7 @@ <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" 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">
 <p>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -815,7 +815,7 @@ <h3 class="callout-title">Exercise 1</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -828,7 +828,7 @@ <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" 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="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -881,7 +881,7 @@ <h3 class="callout-title">Exercise 2</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">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -935,7 +935,7 @@ <h3 class="callout-title">Extension Challenge 1</h3>
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li><p>You have to do tons of book-keeping! If you perform a QC step
@@ -2727,7 +2727,7 @@ <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" 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">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2924,7 +2924,7 @@ <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" 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">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -3222,7 +3222,7 @@ <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" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3486,7 +3486,7 @@ <h3 class="callout-title">Challenge</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="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4526,7 +4526,7 @@ <h3 class="callout-title">Exercise 1: Clustering</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -4543,7 +4543,7 @@ <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="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4582,7 +4582,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</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" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb48">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4655,7 +4655,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -4689,7 +4689,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -4731,7 +4731,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -5024,7 +5024,7 @@ <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
@@ -5090,7 +5090,7 @@ <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>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5544,7 +5544,7 @@ <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. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -5870,7 +5870,7 @@ <h3 class="callout-title">Exercise 1: Replicates</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>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -5884,7 +5884,7 @@ <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>
@@ -5921,7 +5921,7 @@ <h3 class="callout-title">Exercise 2:</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>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -5935,7 +5935,7 @@ <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>
@@ -7251,7 +7251,7 @@ <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 2024-09-24 |
+<p>Last updated on 2024-09-30 |
 
         <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">
@@ -7427,7 +7427,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 $ sample_id_db                      &lt;chr&gt; "0c1d320a7d0cbbc281a535912722d272", …
 $ `_sample_name`                    &lt;chr&gt; "BPH340PrSF_Via___transition zone of…</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="a-note-on-the-piping-operator">A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a>
+</section><section><h2 class="section-heading" id="a-note-on-the-pipe-operator">A note on the pipe operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-pipe-operator"></a>
 </h2>
 <hr class="half-width">
 <p>The vignette materials provided by <code>CuratedAtlasQueryR</code>
@@ -7582,9 +7582,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">sample_subset</span> <span class="op">=</span> <span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">ethnicity</span> <span class="op">==</span> <span class="st">"African"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">tissue</span> <span class="op">==</span> <span class="st">"lung parenchyma"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">cell_type</span>, <span class="st">"%CD4%"</span><span class="op">)</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"CD4"</span>, <span class="va">cell_type</span><span class="op">)</span></span>
 <span>    <span class="op">)</span></span></code></pre>
 </div>
 <div class="section level4">
@@ -7713,12 +7713,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section><h2 class="section-heading" id="exercises">Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a>
 </h2>
 <hr class="half-width">
-<div id="exercise-1" class="callout challenge">
+<div id="exercise-1-basic-counting-piping" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-1" class="callout-inner">
-<h3 class="callout-title">Exercise 1</h3>
+<div id="exercise-1-basic-counting-piping" class="callout-inner">
+<h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <div class="callout-content">
 <p>Use <code>count</code> and <code>arrange</code> to get the number of
 cells per tissue in descending order.</p>
@@ -7730,7 +7730,7 @@ <h3 class="callout-title">Exercise 1</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="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7744,17 +7744,17 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-2" class="callout challenge">
+<div id="exercise-2-tissue-type-counting" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-2" class="callout-inner">
-<h3 class="callout-title">Exercise 2</h3>
+<div id="exercise-2-tissue-type-counting" class="callout-inner">
+<h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <div class="callout-content">
-<p>Use <code>dplyr</code>-isms to group by <code>tissue</code> and
-<code>cell_type</code> and get a tally of the highest number of cell
-types per tissue combination. What tissue has the most numerous type of
-cells?</p>
+<p><code>count()</code> can group by multiple factors by simply adding
+another grouping column as an additional argument. Get a tally of the
+highest number of cell types per tissue combination. What tissue has the
+most numerous type of cells?</p>
 </div>
 </div>
 </div>
@@ -7763,7 +7763,7 @@ <h3 class="callout-title">Exercise 2</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="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7771,18 +7771,19 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="va">cell_type</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>
+<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>
 </div>
 </div>
 </div>
-<div id="exercise-3" class="callout challenge">
+<div id="exercise-3-comparing-metadata-categories" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-3" class="callout-inner">
-<h3 class="callout-title">Exercise 3</h3>
+<div id="exercise-3-comparing-metadata-categories" class="callout-inner">
+<h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <div class="callout-content">
 <p>Spot some differences between the <code>tissue</code> and
 <code>tissue_harmonised</code> columns. Use <code>count</code> to
@@ -7795,7 +7796,7 @@ <h3 class="callout-title">Exercise 3</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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7809,6 +7810,9 @@ <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_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>
+<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>
 <p>To see the full list of curated columns in the metadata, see the
 Details section in the <code>?get_metadata</code> documentation
 page.</p>
@@ -7816,12 +7820,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-4" class="callout challenge">
+<div id="exercise-4-highly-specific-cell-groups" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-4" class="callout-inner">
-<h3 class="callout-title">Exercise 4</h3>
+<div id="exercise-4-highly-specific-cell-groups" class="callout-inner">
+<h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <div class="callout-content">
 <p>Now that we are a little familiar with navigating the metadata, let’s
 obtain a <code>SingleCellExperiment</code> of 10X scRNA-seq counts of
@@ -7836,7 +7840,7 @@ <h3 class="callout-title">Exercise 4</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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7846,7 +7850,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">sex</span> <span class="op">==</span> <span class="st">"female"</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">age_days</span> <span class="op">&gt;</span> <span class="fl">80</span> <span class="op">*</span> <span class="fl">365</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">disease</span> <span class="op">==</span> <span class="st">"COVID-19"</span> <span class="op">&amp;</span>  </span>
 <span>        <span class="va">tissue_harmonised</span> <span class="op">==</span> <span class="st">"lung"</span> <span class="op">&amp;</span> </span>
 <span>        <span class="va">cell_type_harmonised</span> <span class="op">==</span> <span class="st">"cd8 tem"</span></span>
@@ -7869,6 +7873,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mainExpName: NULL
 altExpNames(0):</code></pre>
 </div>
+<p>You can see we don’t get very many cells given the strict set of
+conditions we used.</p>
 </div>
 </div>
 </div>
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diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index d688d3d..b6a63f3 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -516,7 +516,7 @@ <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" 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">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -710,7 +710,7 @@ <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" 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">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1005,7 +1005,7 @@ <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" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1268,7 +1268,7 @@ <h3 class="callout-title">Challenge</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="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2304,7 +2304,7 @@ <h3 class="callout-title">Exercise 1: Clustering</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -2321,7 +2321,7 @@ <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="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2359,7 +2359,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</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" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb48">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2432,7 +2432,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -2466,7 +2466,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -2508,7 +2508,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/hca.html b/hca.html
index 5bdf738..58ebc49 100644
--- a/hca.html
+++ b/hca.html
@@ -269,7 +269,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#installation">Installation</a></li>
 <li><a href="#package-load">Package load</a></li>
 <li><a href="#hca-metadata">HCA Metadata</a></li>
-<li><a href="#a-note-on-the-piping-operator">A note on the piping operator</a></li>
+<li><a href="#a-note-on-the-pipe-operator">A note on the pipe operator</a></li>
 <li><a href="#summarizing-the-metadata">Summarizing the metadata</a></li>
 <li><a href="#columns-available-in-the-metadata">Columns available in the metadata</a></li>
 <li><a href="#available-assays">Available assays</a></li>
@@ -338,7 +338,7 @@ <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 2024-09-24 |
+        <p>Last updated on 2024-09-30 |
 
         <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>
 
@@ -484,7 +484,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 $ sample_id_db                      &lt;chr&gt; "0c1d320a7d0cbbc281a535912722d272", …
 $ `_sample_name`                    &lt;chr&gt; "BPH340PrSF_Via___transition zone of…</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="a-note-on-the-piping-operator">A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a></h2>
+</section><section><h2 class="section-heading" id="a-note-on-the-pipe-operator">A note on the pipe operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-pipe-operator"></a></h2>
 <hr class="half-width"><p>The vignette materials provided by <code>CuratedAtlasQueryR</code>
 show the use of the ‘native’ R pipe (implemented after R version
 <code>4.1.0</code>). For those not familiar with the pipe operator
@@ -630,9 +630,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">sample_subset</span> <span class="op">=</span> <span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">ethnicity</span> <span class="op">==</span> <span class="st">"African"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">tissue</span> <span class="op">==</span> <span class="st">"lung parenchyma"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">cell_type</span>, <span class="st">"%CD4%"</span><span class="op">)</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"CD4"</span>, <span class="va">cell_type</span><span class="op">)</span></span>
 <span>    <span class="op">)</span></span></code></pre>
 </div>
 <div class="section level4">
@@ -753,12 +753,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="exercises">Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a></h2>
-<hr class="half-width"><div id="exercise-1" class="callout challenge">
+<hr class="half-width"><div id="exercise-1-basic-counting-piping" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-1" class="callout-inner">
-<h3 class="callout-title">Exercise 1</h3>
+<div id="exercise-1-basic-counting-piping" class="callout-inner">
+<h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <div class="callout-content">
 <p>Use <code>count</code> and <code>arrange</code> to get the number of
 cells per tissue in descending order.</p>
@@ -770,7 +770,7 @@ <h3 class="callout-title">Exercise 1</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="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -784,17 +784,17 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-2" class="callout challenge">
+<div id="exercise-2-tissue-type-counting" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-2" class="callout-inner">
-<h3 class="callout-title">Exercise 2</h3>
+<div id="exercise-2-tissue-type-counting" class="callout-inner">
+<h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <div class="callout-content">
-<p>Use <code>dplyr</code>-isms to group by <code>tissue</code> and
-<code>cell_type</code> and get a tally of the highest number of cell
-types per tissue combination. What tissue has the most numerous type of
-cells?</p>
+<p><code>count()</code> can group by multiple factors by simply adding
+another grouping column as an additional argument. Get a tally of the
+highest number of cell types per tissue combination. What tissue has the
+most numerous type of cells?</p>
 </div>
 </div>
 </div>
@@ -803,7 +803,7 @@ <h3 class="callout-title">Exercise 2</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="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -811,18 +811,19 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="va">cell_type</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>
+<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>
 </div>
 </div>
 </div>
-<div id="exercise-3" class="callout challenge">
+<div id="exercise-3-comparing-metadata-categories" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-3" class="callout-inner">
-<h3 class="callout-title">Exercise 3</h3>
+<div id="exercise-3-comparing-metadata-categories" class="callout-inner">
+<h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <div class="callout-content">
 <p>Spot some differences between the <code>tissue</code> and
 <code>tissue_harmonised</code> columns. Use <code>count</code> to
@@ -835,7 +836,7 @@ <h3 class="callout-title">Exercise 3</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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -849,6 +850,9 @@ <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_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>
+<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>
 <p>To see the full list of curated columns in the metadata, see the
 Details section in the <code>?get_metadata</code> documentation
 page.</p>
@@ -856,12 +860,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-4" class="callout challenge">
+<div id="exercise-4-highly-specific-cell-groups" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-4" class="callout-inner">
-<h3 class="callout-title">Exercise 4</h3>
+<div id="exercise-4-highly-specific-cell-groups" class="callout-inner">
+<h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <div class="callout-content">
 <p>Now that we are a little familiar with navigating the metadata, let’s
 obtain a <code>SingleCellExperiment</code> of 10X scRNA-seq counts of
@@ -876,7 +880,7 @@ <h3 class="callout-title">Exercise 4</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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -886,7 +890,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">sex</span> <span class="op">==</span> <span class="st">"female"</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">age_days</span> <span class="op">&gt;</span> <span class="fl">80</span> <span class="op">*</span> <span class="fl">365</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">disease</span> <span class="op">==</span> <span class="st">"COVID-19"</span> <span class="op">&amp;</span>  </span>
 <span>        <span class="va">tissue_harmonised</span> <span class="op">==</span> <span class="st">"lung"</span> <span class="op">&amp;</span> </span>
 <span>        <span class="va">cell_type_harmonised</span> <span class="op">==</span> <span class="st">"cd8 tem"</span></span>
@@ -909,6 +913,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mainExpName: NULL
 altExpNames(0):</code></pre>
 </div>
+<p>You can see we don’t get very many cells given the strict set of
+conditions we used.</p>
 </div>
 </div>
 </div>
@@ -990,7 +996,7 @@ <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": "2024-09-24",
+  "dateModified": "2024-09-30",
   "datePublished": "2024-09-30"
 }
 
diff --git a/instructor/aio.html b/instructor/aio.html
index b4024f5..b26ee29 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -593,7 +593,7 @@ <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" 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">
 <p>Here we assign the sixth sample to <code>sce6</code>:</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -738,7 +738,7 @@ <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" 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">
 <p>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -818,7 +818,7 @@ <h3 class="callout-title">Exercise 1</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -831,7 +831,7 @@ <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" 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="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -884,7 +884,7 @@ <h3 class="callout-title">Exercise 2</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">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -938,7 +938,7 @@ <h3 class="callout-title">Extension Challenge 1</h3>
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li><p>You have to do tons of book-keeping! If you perform a QC step
@@ -2732,7 +2732,7 @@ <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" 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">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2929,7 +2929,7 @@ <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" 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">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -3227,7 +3227,7 @@ <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" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3491,7 +3491,7 @@ <h3 class="callout-title">Challenge</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="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4531,7 +4531,7 @@ <h3 class="callout-title">Exercise 1: Clustering</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -4548,7 +4548,7 @@ <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="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4587,7 +4587,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</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" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb48">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4660,7 +4660,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -4694,7 +4694,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -4736,7 +4736,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -5030,7 +5030,7 @@ <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
@@ -5096,7 +5096,7 @@ <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>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -5550,7 +5550,7 @@ <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. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -5876,7 +5876,7 @@ <h3 class="callout-title">Exercise 1: Replicates</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>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -5890,7 +5890,7 @@ <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>
@@ -5927,7 +5927,7 @@ <h3 class="callout-title">Exercise 2:</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>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -5941,7 +5941,7 @@ <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>
@@ -7258,7 +7258,7 @@ <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 2024-09-24 |
+<p>Last updated on 2024-09-30 |
 
         <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>
@@ -7435,7 +7435,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 $ sample_id_db                      &lt;chr&gt; "0c1d320a7d0cbbc281a535912722d272", …
 $ `_sample_name`                    &lt;chr&gt; "BPH340PrSF_Via___transition zone of…</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="a-note-on-the-piping-operator">A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a>
+</section><section><h2 class="section-heading" id="a-note-on-the-pipe-operator">A note on the pipe operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-pipe-operator"></a>
 </h2>
 <hr class="half-width">
 <p>The vignette materials provided by <code>CuratedAtlasQueryR</code>
@@ -7590,9 +7590,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">sample_subset</span> <span class="op">=</span> <span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">ethnicity</span> <span class="op">==</span> <span class="st">"African"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">tissue</span> <span class="op">==</span> <span class="st">"lung parenchyma"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">cell_type</span>, <span class="st">"%CD4%"</span><span class="op">)</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"CD4"</span>, <span class="va">cell_type</span><span class="op">)</span></span>
 <span>    <span class="op">)</span></span></code></pre>
 </div>
 <div class="section level4">
@@ -7721,12 +7721,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section><h2 class="section-heading" id="exercises">Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a>
 </h2>
 <hr class="half-width">
-<div id="exercise-1" class="callout challenge">
+<div id="exercise-1-basic-counting-piping" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-1" class="callout-inner">
-<h3 class="callout-title">Exercise 1</h3>
+<div id="exercise-1-basic-counting-piping" class="callout-inner">
+<h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <div class="callout-content">
 <p>Use <code>count</code> and <code>arrange</code> to get the number of
 cells per tissue in descending order.</p>
@@ -7738,7 +7738,7 @@ <h3 class="callout-title">Exercise 1</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="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7752,17 +7752,17 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-2" class="callout challenge">
+<div id="exercise-2-tissue-type-counting" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-2" class="callout-inner">
-<h3 class="callout-title">Exercise 2</h3>
+<div id="exercise-2-tissue-type-counting" class="callout-inner">
+<h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <div class="callout-content">
-<p>Use <code>dplyr</code>-isms to group by <code>tissue</code> and
-<code>cell_type</code> and get a tally of the highest number of cell
-types per tissue combination. What tissue has the most numerous type of
-cells?</p>
+<p><code>count()</code> can group by multiple factors by simply adding
+another grouping column as an additional argument. Get a tally of the
+highest number of cell types per tissue combination. What tissue has the
+most numerous type of cells?</p>
 </div>
 </div>
 </div>
@@ -7771,7 +7771,7 @@ <h3 class="callout-title">Exercise 2</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="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7779,18 +7779,19 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="va">cell_type</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>
+<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>
 </div>
 </div>
 </div>
-<div id="exercise-3" class="callout challenge">
+<div id="exercise-3-comparing-metadata-categories" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-3" class="callout-inner">
-<h3 class="callout-title">Exercise 3</h3>
+<div id="exercise-3-comparing-metadata-categories" class="callout-inner">
+<h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <div class="callout-content">
 <p>Spot some differences between the <code>tissue</code> and
 <code>tissue_harmonised</code> columns. Use <code>count</code> to
@@ -7803,7 +7804,7 @@ <h3 class="callout-title">Exercise 3</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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7817,6 +7818,9 @@ <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_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>
+<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>
 <p>To see the full list of curated columns in the metadata, see the
 Details section in the <code>?get_metadata</code> documentation
 page.</p>
@@ -7824,12 +7828,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-4" class="callout challenge">
+<div id="exercise-4-highly-specific-cell-groups" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-4" class="callout-inner">
-<h3 class="callout-title">Exercise 4</h3>
+<div id="exercise-4-highly-specific-cell-groups" class="callout-inner">
+<h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <div class="callout-content">
 <p>Now that we are a little familiar with navigating the metadata, let’s
 obtain a <code>SingleCellExperiment</code> of 10X scRNA-seq counts of
@@ -7844,7 +7848,7 @@ <h3 class="callout-title">Exercise 4</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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7854,7 +7858,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">sex</span> <span class="op">==</span> <span class="st">"female"</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">age_days</span> <span class="op">&gt;</span> <span class="fl">80</span> <span class="op">*</span> <span class="fl">365</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">disease</span> <span class="op">==</span> <span class="st">"COVID-19"</span> <span class="op">&amp;</span>  </span>
 <span>        <span class="va">tissue_harmonised</span> <span class="op">==</span> <span class="st">"lung"</span> <span class="op">&amp;</span> </span>
 <span>        <span class="va">cell_type_harmonised</span> <span class="op">==</span> <span class="st">"cd8 tem"</span></span>
@@ -7877,6 +7881,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mainExpName: NULL
 altExpNames(0):</code></pre>
 </div>
+<p>You can see we don’t get very many cells given the strict set of
+conditions we used.</p>
 </div>
 </div>
 </div>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 341c955..b7dcab7 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -518,7 +518,7 @@ <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" 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">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -712,7 +712,7 @@ <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" 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">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1007,7 +1007,7 @@ <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" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1270,7 +1270,7 @@ <h3 class="callout-title">Challenge</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="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2306,7 +2306,7 @@ <h3 class="callout-title">Exercise 1: Clustering</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -2323,7 +2323,7 @@ <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="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2361,7 +2361,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</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" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb48">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2434,7 +2434,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -2468,7 +2468,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -2510,7 +2510,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
diff --git a/instructor/hca.html b/instructor/hca.html
index 5f14cea..a256fcc 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -269,7 +269,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#installation">Installation</a></li>
 <li><a href="#package-load">Package load</a></li>
 <li><a href="#hca-metadata">HCA Metadata</a></li>
-<li><a href="#a-note-on-the-piping-operator">A note on the piping operator</a></li>
+<li><a href="#a-note-on-the-pipe-operator">A note on the pipe operator</a></li>
 <li><a href="#summarizing-the-metadata">Summarizing the metadata</a></li>
 <li><a href="#columns-available-in-the-metadata">Columns available in the metadata</a></li>
 <li><a href="#available-assays">Available assays</a></li>
@@ -338,7 +338,7 @@ <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 2024-09-24 |
+        <p>Last updated on 2024-09-30 |
 
         <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>
 
@@ -486,7 +486,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 $ sample_id_db                      &lt;chr&gt; "0c1d320a7d0cbbc281a535912722d272", …
 $ `_sample_name`                    &lt;chr&gt; "BPH340PrSF_Via___transition zone of…</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="a-note-on-the-piping-operator">A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a></h2>
+</section><section><h2 class="section-heading" id="a-note-on-the-pipe-operator">A note on the pipe operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-pipe-operator"></a></h2>
 <hr class="half-width"><p>The vignette materials provided by <code>CuratedAtlasQueryR</code>
 show the use of the ‘native’ R pipe (implemented after R version
 <code>4.1.0</code>). For those not familiar with the pipe operator
@@ -632,9 +632,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="va">sample_subset</span> <span class="op">=</span> <span class="va">metadata</span> <span class="op">|&gt;</span></span>
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">ethnicity</span> <span class="op">==</span> <span class="st">"African"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">tissue</span> <span class="op">==</span> <span class="st">"lung parenchyma"</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">cell_type</span>, <span class="st">"%CD4%"</span><span class="op">)</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"CD4"</span>, <span class="va">cell_type</span><span class="op">)</span></span>
 <span>    <span class="op">)</span></span></code></pre>
 </div>
 <div class="section level4">
@@ -755,12 +755,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="exercises">Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a></h2>
-<hr class="half-width"><div id="exercise-1" class="callout challenge">
+<hr class="half-width"><div id="exercise-1-basic-counting-piping" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-1" class="callout-inner">
-<h3 class="callout-title">Exercise 1</h3>
+<div id="exercise-1-basic-counting-piping" class="callout-inner">
+<h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <div class="callout-content">
 <p>Use <code>count</code> and <code>arrange</code> to get the number of
 cells per tissue in descending order.</p>
@@ -772,7 +772,7 @@ <h3 class="callout-title">Exercise 1</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="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -786,17 +786,17 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-2" class="callout challenge">
+<div id="exercise-2-tissue-type-counting" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-2" class="callout-inner">
-<h3 class="callout-title">Exercise 2</h3>
+<div id="exercise-2-tissue-type-counting" class="callout-inner">
+<h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <div class="callout-content">
-<p>Use <code>dplyr</code>-isms to group by <code>tissue</code> and
-<code>cell_type</code> and get a tally of the highest number of cell
-types per tissue combination. What tissue has the most numerous type of
-cells?</p>
+<p><code>count()</code> can group by multiple factors by simply adding
+another grouping column as an additional argument. Get a tally of the
+highest number of cell types per tissue combination. What tissue has the
+most numerous type of cells?</p>
 </div>
 </div>
 </div>
@@ -805,7 +805,7 @@ <h3 class="callout-title">Exercise 2</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="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -813,18 +813,19 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="va">cell_type</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>
+<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>
 </div>
 </div>
 </div>
-<div id="exercise-3" class="callout challenge">
+<div id="exercise-3-comparing-metadata-categories" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-3" class="callout-inner">
-<h3 class="callout-title">Exercise 3</h3>
+<div id="exercise-3-comparing-metadata-categories" class="callout-inner">
+<h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <div class="callout-content">
 <p>Spot some differences between the <code>tissue</code> and
 <code>tissue_harmonised</code> columns. Use <code>count</code> to
@@ -837,7 +838,7 @@ <h3 class="callout-title">Exercise 3</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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -851,6 +852,9 @@ <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_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>
+<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>
 <p>To see the full list of curated columns in the metadata, see the
 Details section in the <code>?get_metadata</code> documentation
 page.</p>
@@ -858,12 +862,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-<div id="exercise-4" class="callout challenge">
+<div id="exercise-4-highly-specific-cell-groups" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
 </div>
-<div id="exercise-4" class="callout-inner">
-<h3 class="callout-title">Exercise 4</h3>
+<div id="exercise-4-highly-specific-cell-groups" class="callout-inner">
+<h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <div class="callout-content">
 <p>Now that we are a little familiar with navigating the metadata, let’s
 obtain a <code>SingleCellExperiment</code> of 10X scRNA-seq counts of
@@ -878,7 +882,7 @@ <h3 class="callout-title">Exercise 4</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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -888,7 +892,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    <span class="fu">filter</span><span class="op">(</span></span>
 <span>        <span class="va">sex</span> <span class="op">==</span> <span class="st">"female"</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">age_days</span> <span class="op">&gt;</span> <span class="fl">80</span> <span class="op">*</span> <span class="fl">365</span> <span class="op">&amp;</span></span>
-<span>        <span class="fu">stringr</span><span class="fu">::</span><span class="fu">str_like</span><span class="op">(</span><span class="va">assay</span>, <span class="st">"%10x%"</span><span class="op">)</span> <span class="op">&amp;</span></span>
+<span>        <span class="fu">grepl</span><span class="op">(</span><span class="st">"10x"</span>, <span class="va">assay</span><span class="op">)</span> <span class="op">&amp;</span></span>
 <span>        <span class="va">disease</span> <span class="op">==</span> <span class="st">"COVID-19"</span> <span class="op">&amp;</span>  </span>
 <span>        <span class="va">tissue_harmonised</span> <span class="op">==</span> <span class="st">"lung"</span> <span class="op">&amp;</span> </span>
 <span>        <span class="va">cell_type_harmonised</span> <span class="op">==</span> <span class="st">"cd8 tem"</span></span>
@@ -911,6 +915,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mainExpName: NULL
 altExpNames(0):</code></pre>
 </div>
+<p>You can see we don’t get very many cells given the strict set of
+conditions we used.</p>
 </div>
 </div>
 </div>
@@ -992,7 +998,7 @@ <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": "2024-09-24",
+  "dateModified": "2024-09-30",
   "datePublished": "2024-09-30"
 }
 
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index a98743f..b4cff5a 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.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" 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">
 <p>Here we assign the sixth sample to <code>sce6</code>:</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -685,7 +685,7 @@ <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" 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">
 <p>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -764,7 +764,7 @@ <h3 class="callout-title">Exercise 1</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -777,7 +777,7 @@ <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" 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="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -830,7 +830,7 @@ <h3 class="callout-title">Exercise 2</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">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -884,7 +884,7 @@ <h3 class="callout-title">Extension Challenge 1</h3>
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>You have to do tons of book-keeping! If you perform a QC step
 that removes dead cells, now you also have to remember to remove that
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 8866759..d6d5f59 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
@@ -609,7 +609,7 @@ <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>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -1059,7 +1059,7 @@ <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. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -1376,7 +1376,7 @@ <h3 class="callout-title">Exercise 1: Replicates</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>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -1390,7 +1390,7 @@ <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>
@@ -1427,7 +1427,7 @@ <h3 class="callout-title">Exercise 2:</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>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -1441,7 +1441,7 @@ <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>
diff --git a/intro-sce.html b/intro-sce.html
index 8860844..3ee2746 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -541,7 +541,7 @@ <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" 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">
 <p>Here we assign the sixth sample to <code>sce6</code>:</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -683,7 +683,7 @@ <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" 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">
 <p>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -762,7 +762,7 @@ <h3 class="callout-title">Exercise 1</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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -775,7 +775,7 @@ <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" 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="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -828,7 +828,7 @@ <h3 class="callout-title">Exercise 2</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">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -882,7 +882,7 @@ <h3 class="callout-title">Extension Challenge 1</h3>
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>You have to do tons of book-keeping! If you perform a QC step
 that removes dead cells, now you also have to remember to remove that
diff --git a/md5sum.txt b/md5sum.txt
index 94030b4..c01b248 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -9,7 +9,7 @@
 "episodes/cell_type_annotation.Rmd" "dc23fda097f772bec1b7172277298221" "site/built/cell_type_annotation.md" "2024-09-30"
 "episodes/multi-sample.Rmd" "2d38d9903358ea8a8067abd82a1f1f54" "site/built/multi-sample.md" "2024-09-24"
 "episodes/large_data.Rmd" "b9710492c6792ea435778c4e42f27e02" "site/built/large_data.md" "2024-09-24"
-"episodes/hca.Rmd" "e01d3fd1e07f158bed08b72d657ae1d1" "site/built/hca.md" "2024-09-24"
+"episodes/hca.Rmd" "20f753a47fcae8ed5d0631fbc582f549" "site/built/hca.md" "2024-09-30"
 "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 f667b4c..9ae348e 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
@@ -607,7 +607,7 @@ <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>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -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">
   <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. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -1374,7 +1374,7 @@ <h3 class="callout-title">Exercise 1: Replicates</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>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -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">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1425,7 +1425,7 @@ <h3 class="callout-title">Exercise 2:</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>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -1439,7 +1439,7 @@ <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>
diff --git a/pkgdown.yml b/pkgdown.yml
index 1937c0d..9970d75 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-09-30T14:47Z
+last_built: 2024-09-30T15:44Z