From 61994f0e7fe0823dee2669d5a7724b473a8f5116 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 20 Aug 2024 01:10:48 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : c84057b8f4057b8d2dbe6c3a072454574d51b3fb
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-08-19 18:00:14 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 4426fa5565f5e3f40b82f78e0e29abca519e2a68
Branch  : main
Author  : Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Time    : 2024-08-19 17:16:49 +0000
Message : Merge pull request #19 from ccb-hms/add_exercises

Add exercises
---
 404.html                             |  4 +-
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE.html                         |  2 +-
 aio.html                             | 62 ++++++++++++++--------------
 cell_type_annotation.html            | 20 ++++-----
 eda_qc.html                          |  2 +-
 hca.html                             | 10 ++---
 images.html                          |  4 +-
 index.html                           |  4 +-
 instructor-notes.html                |  4 +-
 instructor/404.html                  |  4 +-
 instructor/CODE_OF_CONDUCT.html      |  2 +-
 instructor/LICENSE.html              |  2 +-
 instructor/aio.html                  | 62 ++++++++++++++--------------
 instructor/cell_type_annotation.html | 20 ++++-----
 instructor/eda_qc.html               |  2 +-
 instructor/hca.html                  | 10 ++---
 instructor/images.html               |  4 +-
 instructor/index.html                |  4 +-
 instructor/instructor-notes.html     |  4 +-
 instructor/intro-sce.html            |  8 ++--
 instructor/key-points.html           |  4 +-
 instructor/large_data.html           | 14 +++----
 instructor/multi-sample.html         | 16 +++----
 instructor/profiles.html             |  4 +-
 instructor/reference.html            |  2 +-
 intro-sce.html                       |  8 ++--
 key-points.html                      |  4 +-
 large_data.html                      | 14 +++----
 multi-sample.html                    | 16 +++----
 pkgdown.yml                          |  2 +-
 profiles.html                        |  4 +-
 reference.html                       |  2 +-
 33 files changed, 163 insertions(+), 163 deletions(-)

diff --git a/404.html b/404.html
index 09b719d..308ae4d 100644
--- a/404.html
+++ b/404.html
@@ -377,8 +377,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 5faa0ca..14be4b2 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -399,7 +399,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index b2b2174..b766fce 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -450,7 +450,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index fb6442b..727eb1a 100644
--- a/aio.html
+++ b/aio.html
@@ -588,7 +588,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <ol style="list-style-type: decimal">
 <li><p>You have to do tons of book-keeping! If you perform a QC step
@@ -733,7 +733,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -810,7 +810,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -2344,7 +2344,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -2497,7 +2497,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>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
@@ -2793,7 +2793,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <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
@@ -3253,7 +3253,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -3405,7 +3405,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <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
@@ -3422,7 +3422,7 @@ <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">
 <p>TODO</p>
 </div>
@@ -3452,7 +3452,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3466,7 +3466,7 @@ <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="#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">
 <p>TODO</p>
 </div>
@@ -3497,7 +3497,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <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>TODO</p>
 </div>
@@ -3779,7 +3779,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -3846,7 +3846,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -4290,7 +4290,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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.
@@ -4613,7 +4613,7 @@ <h3 class="callout-title">Exercise 1: Replicates<a class="anchor" aria-label="an
 <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
@@ -4627,7 +4627,7 @@ <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>
@@ -4664,7 +4664,7 @@ <h3 class="callout-title">Exercise 2:<a class="anchor" aria-label="anchor" href=
 <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
@@ -4678,7 +4678,7 @@ <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>
@@ -5636,7 +5636,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5650,7 +5650,7 @@ <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="#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>TODO</p>
 </div>
@@ -5678,7 +5678,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5691,7 +5691,7 @@ <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="#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>TODO</p>
 </div>
@@ -5721,7 +5721,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5733,7 +5733,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -6297,7 +6297,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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">
 <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>
@@ -6331,7 +6331,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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">
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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@@ -6519,8 +6519,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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-  "dateModified": "2024-08-19",
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diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 9fd35b6..12592ea 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -512,7 +512,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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 </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
@@ -663,7 +663,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <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
@@ -956,7 +956,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <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
@@ -1415,7 +1415,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
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 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
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@@ -1563,7 +1563,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
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 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
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@@ -1580,7 +1580,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <p>TODO</p>
 </div>
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 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
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 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
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 </button>
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 <div class="accordion-body">
 <p>TODO</p>
 </div>
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 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
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 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1782,7 +1782,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/eda_qc.html b/eda_qc.html
index f1aa56b..a3959de 100644
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diff --git a/hca.html b/hca.html
index a363864..3a97cf8 100644
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="codewrapper sourceCode" id="cb24">
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@@ -831,7 +831,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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@@ -865,7 +865,7 @@ <h3 class="callout-title">Exercise 3<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
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@@ -907,7 +907,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
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 </button>
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@@ -1029,7 +1029,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/images.html b/images.html
index a869d01..2c4840c 100644
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-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
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diff --git a/index.html b/index.html
index 72f916c..94dd383 100644
--- a/index.html
+++ b/index.html
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-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
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+  "datePublished": "2024-08-20"
 }
 
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diff --git a/instructor-notes.html b/instructor-notes.html
index a990616..9d79e81 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -422,8 +422,8 @@ <h1>Instructor Notes</h1>
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-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 16bce34..ea20593 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -377,8 +377,8 @@ <h1>Page not found</h1>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 22ad17d..0d2eab2 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -401,7 +401,7 @@ <h1>Contributor Code of Conduct</h1>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index e9bcfe5..d83c185 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -452,7 +452,7 @@ <h1>Licenses</h1>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
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diff --git a/instructor/aio.html b/instructor/aio.html
index b821312..263c146 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <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
@@ -736,7 +736,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <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>
@@ -813,7 +813,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -2349,7 +2349,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -2502,7 +2502,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>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
@@ -2798,7 +2798,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <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
@@ -3258,7 +3258,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -3410,7 +3410,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <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
@@ -3427,7 +3427,7 @@ <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">
 <p>TODO</p>
 </div>
@@ -3457,7 +3457,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
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 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3471,7 +3471,7 @@ <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="#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">
 <p>TODO</p>
 </div>
@@ -3502,7 +3502,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <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>TODO</p>
 </div>
@@ -3785,7 +3785,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -3852,7 +3852,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -4296,7 +4296,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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.
@@ -4619,7 +4619,7 @@ <h3 class="callout-title">Exercise 1: Replicates<a class="anchor" aria-label="an
 <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
@@ -4633,7 +4633,7 @@ <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">
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 <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>
@@ -4670,7 +4670,7 @@ <h3 class="callout-title">Exercise 2:<a class="anchor" aria-label="anchor" href=
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
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 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -4684,7 +4684,7 @@ <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>
@@ -5643,7 +5643,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5657,7 +5657,7 @@ <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="#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>TODO</p>
 </div>
@@ -5685,7 +5685,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
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 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5698,7 +5698,7 @@ <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="#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>TODO</p>
 </div>
@@ -5728,7 +5728,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
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 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5740,7 +5740,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -6305,7 +6305,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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">
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 <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>
@@ -6339,7 +6339,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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">
 <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>
@@ -6373,7 +6373,7 @@ <h3 class="callout-title">Exercise 3<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6415,7 +6415,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
 <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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6527,8 +6527,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index a36de11..ba6f965 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -514,7 +514,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -665,7 +665,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>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
@@ -958,7 +958,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <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
@@ -1417,7 +1417,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -1565,7 +1565,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <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
@@ -1582,7 +1582,7 @@ <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">
 <p>TODO</p>
 </div>
@@ -1612,7 +1612,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1626,7 +1626,7 @@ <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="#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">
 <p>TODO</p>
 </div>
@@ -1657,7 +1657,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <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>TODO</p>
 </div>
@@ -1784,7 +1784,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 96c0455..9c838f7 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
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+  "datePublished": "2024-08-20"
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   </script><script>
diff --git a/instructor/hca.html b/instructor/hca.html
index a5d3f6f..cb2a89b 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -799,7 +799,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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">
 <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>
@@ -833,7 +833,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <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">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
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@@ -867,7 +867,7 @@ <h3 class="callout-title">Exercise 3<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
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@@ -909,7 +909,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
 <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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1031,7 +1031,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
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diff --git a/instructor/images.html b/instructor/images.html
index 0957a16..a85113a 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -492,8 +492,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index c3be229..977aec9 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -669,8 +669,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index a30c053..ceae113 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -430,8 +430,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index d847861..f826b07 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -542,7 +542,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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   <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">
 <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
@@ -682,7 +682,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -878,7 +878,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 386bd47..27446f1 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -540,8 +540,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 4d30bcf..0022254 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -1198,7 +1198,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1212,7 +1212,7 @@ <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="#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>TODO</p>
 </div>
@@ -1240,7 +1240,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1253,7 +1253,7 @@ <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="#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>TODO</p>
 </div>
@@ -1283,7 +1283,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1295,7 +1295,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1403,7 +1403,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 58013f2..63d083f 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -539,7 +539,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -604,7 +604,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -1044,7 +1044,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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.
@@ -1358,7 +1358,7 @@ <h3 class="callout-title">Exercise 1: Replicates<a class="anchor" aria-label="an
 <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
@@ -1372,7 +1372,7 @@ <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>
@@ -1409,7 +1409,7 @@ <h3 class="callout-title">Exercise 2:<a class="anchor" aria-label="anchor" href=
 <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
@@ -1423,7 +1423,7 @@ <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>
@@ -1553,7 +1553,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index aedd197..b47e26c 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -352,8 +352,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 95844c2..8e59eb2 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -414,7 +414,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index d7c616f..81bb3a1 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -540,7 +540,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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">
 <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
@@ -680,7 +680,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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>Here we add a column called “conservation” that is just an integer
 sequence from 1 to the number of genes.</p>
@@ -756,7 +756,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <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>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -876,7 +876,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 27e3a95..027e73c 100644
--- a/key-points.html
+++ b/key-points.html
@@ -538,8 +538,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index b773e91..3cab154 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1196,7 +1196,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1210,7 +1210,7 @@ <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="#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>TODO</p>
 </div>
@@ -1238,7 +1238,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1251,7 +1251,7 @@ <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="#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>TODO</p>
 </div>
@@ -1281,7 +1281,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1293,7 +1293,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1401,7 +1401,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/multi-sample.html b/multi-sample.html
index a627dcd..0acc757 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -537,7 +537,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -602,7 +602,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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
@@ -1042,7 +1042,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <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.
@@ -1356,7 +1356,7 @@ <h3 class="callout-title">Exercise 1: Replicates<a class="anchor" aria-label="an
 <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
@@ -1370,7 +1370,7 @@ <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>
@@ -1407,7 +1407,7 @@ <h3 class="callout-title">Exercise 2:<a class="anchor" aria-label="anchor" href=
 <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
@@ -1421,7 +1421,7 @@ <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>
@@ -1551,7 +1551,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 9abdc02..1a68142 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-19T18:01Z
+last_built: 2024-08-20T01:10Z
diff --git a/profiles.html b/profiles.html
index f2ccf77..60548fa 100644
--- a/profiles.html
+++ b/profiles.html
@@ -352,8 +352,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-19",
-  "datePublished": "2024-08-19"
+  "dateModified": "2024-08-20",
+  "datePublished": "2024-08-20"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 4576422..725ff1c 100644
--- a/reference.html
+++ b/reference.html
@@ -412,7 +412,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-19"
+  "datePublished": "2024-08-20"
 }
 
   </script><script>