From abbcc055a5879a4bbf42e74a1537c5463f6afc98 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 3 Sep 2024 01:14:35 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 4cf89b728e79dd1da66f704dc5894fd27c979c6f
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-08-26 19:27:50 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 63249ba34e6be0252407ccf1b9c0e4a7c884b038
Branch  : main
Author  : Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Time    : 2024-08-26 18:33:30 +0000
Message : Merge pull request #21 from ccb-hms/add_exercises

Add exercises
---
 404.html                             |  4 +-
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE.html                         |  2 +-
 aio.html                             | 56 ++++++++++++++--------------
 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                  | 56 ++++++++++++++--------------
 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            |  2 +-
 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                       |  2 +-
 key-points.html                      |  4 +-
 large_data.html                      | 14 +++----
 multi-sample.html                    | 16 ++++----
 pkgdown.yml                          |  2 +-
 profiles.html                        |  4 +-
 reference.html                       |  2 +-
 33 files changed, 151 insertions(+), 151 deletions(-)

diff --git a/404.html b/404.html
index dcff4a4..f5512ed 100644
--- a/404.html
+++ b/404.html
@@ -376,8 +376,8 @@ <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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index a202d1a..11c5cde 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": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 55b74b8..521ca83 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -447,7 +447,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 4e6427f..b5f5b76 100644
--- a/aio.html
+++ b/aio.html
@@ -2312,7 +2312,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2463,7 +2463,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>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
@@ -2757,7 +2757,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>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
@@ -3216,7 +3216,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -3365,7 +3365,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3382,7 +3382,7 @@ <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" 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">
 <p>TODO</p>
 </div>
@@ -3411,7 +3411,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <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
@@ -3425,7 +3425,7 @@ <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" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3455,7 +3455,7 @@ <h3 class="callout-title">Exercise 3: Workflow</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3733,7 +3733,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -3798,7 +3798,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -4240,7 +4240,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -4559,7 +4559,7 @@ <h3 class="callout-title">Exercise 1: Replicates</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -4573,7 +4573,7 @@ <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>
@@ -4609,7 +4609,7 @@ <h3 class="callout-title">Exercise 2:</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -4623,7 +4623,7 @@ <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>
@@ -5103,7 +5103,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -5312,7 +5312,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -5709,7 +5709,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5723,7 +5723,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb49">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5802,7 +5802,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5815,7 +5815,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb55">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6384,7 +6384,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6417,7 +6417,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6449,7 +6449,7 @@ <h3 class="callout-title">Exercise 3</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6490,7 +6490,7 @@ <h3 class="callout-title">Exercise 4</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6596,8 +6596,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/aio.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 67cb877..184d5b2 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -507,7 +507,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -656,7 +656,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>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
@@ -947,7 +947,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>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
@@ -1405,7 +1405,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -1550,7 +1550,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1567,7 +1567,7 @@ <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" 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">
 <p>TODO</p>
 </div>
@@ -1596,7 +1596,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <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
@@ -1610,7 +1610,7 @@ <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" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1640,7 +1640,7 @@ <h3 class="callout-title">Exercise 3: Workflow</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1765,7 +1765,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index a7d555d..050b648 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -1619,7 +1619,7 @@ <h3 class="callout-title">Further Reading</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/hca.html b/hca.html
index db28161..49f5483 100644
--- a/hca.html
+++ b/hca.html
@@ -788,7 +788,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -821,7 +821,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -853,7 +853,7 @@ <h3 class="callout-title">Exercise 3</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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="cb29">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -894,7 +894,7 @@ <h3 class="callout-title">Exercise 4</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1009,7 +1009,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-26",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 6d74a12..40f0978 100644
--- a/images.html
+++ b/images.html
@@ -492,8 +492,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 6103a22..b979a9c 100644
--- a/index.html
+++ b/index.html
@@ -584,8 +584,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
   "url": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index e60bdc6..c8812a7 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -422,8 +422,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 4058ab4..b2b3814 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -376,8 +376,8 @@ <h1>Page not found</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index eed0c2e..4780bdf 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -401,7 +401,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 2c5b92b..411e4de 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -449,7 +449,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index f722ebb..b5c50af 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -2317,7 +2317,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2468,7 +2468,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>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
@@ -2762,7 +2762,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>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
@@ -3221,7 +3221,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -3370,7 +3370,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3387,7 +3387,7 @@ <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" 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">
 <p>TODO</p>
 </div>
@@ -3416,7 +3416,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <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
@@ -3430,7 +3430,7 @@ <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" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3460,7 +3460,7 @@ <h3 class="callout-title">Exercise 3: Workflow</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3739,7 +3739,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -3804,7 +3804,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -4246,7 +4246,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -4565,7 +4565,7 @@ <h3 class="callout-title">Exercise 1: Replicates</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -4579,7 +4579,7 @@ <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">
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 </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>
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 <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>
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+<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
@@ -4629,7 +4629,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5110,7 +5110,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -5319,7 +5319,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -5716,7 +5716,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5730,7 +5730,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb49">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5809,7 +5809,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
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 </button>
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 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5822,7 +5822,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
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 </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="cb55">
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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">
   <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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6425,7 +6425,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb28">
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@@ -6457,7 +6457,7 @@ <h3 class="callout-title">Exercise 3</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
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@@ -6498,7 +6498,7 @@ <h3 class="callout-title">Exercise 4</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6604,8 +6604,8 @@ <h3 class="callout-title">Key Points</h3>
   "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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 06f3313..0dfb531 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -509,7 +509,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -658,7 +658,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>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
@@ -949,7 +949,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>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
@@ -1407,7 +1407,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -1552,7 +1552,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1569,7 +1569,7 @@ <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" 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">
 <p>TODO</p>
 </div>
@@ -1598,7 +1598,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <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
@@ -1612,7 +1612,7 @@ <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" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1642,7 +1642,7 @@ <h3 class="callout-title">Exercise 3: Workflow</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1767,7 +1767,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 5f31834..c2fa0a0 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -1621,7 +1621,7 @@ <h3 class="callout-title">Further Reading</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/hca.html b/instructor/hca.html
index dca650d..06b194f 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -790,7 +790,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -823,7 +823,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb28">
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@@ -855,7 +855,7 @@ <h3 class="callout-title">Exercise 3</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
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@@ -896,7 +896,7 @@ <h3 class="callout-title">Exercise 4</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb30">
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@@ -1011,7 +1011,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-26",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 8ca9cf6..5078055 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -494,8 +494,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 7090bf3..c37dd4a 100644
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+++ 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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index e685b53..a8972f5 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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index ea4f089..1d8082d 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -869,7 +869,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index a109f7b..de3f3c3 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -540,8 +540,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/large_data.html b/instructor/large_data.html
index dd69a81..986428f 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -734,7 +734,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -939,7 +939,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1328,7 +1328,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1342,7 +1342,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb49">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1421,7 +1421,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1434,7 +1434,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb55">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1556,7 +1556,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-26",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index a737811..69e15cb 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -537,7 +537,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -600,7 +600,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -1038,7 +1038,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -1348,7 +1348,7 @@ <h3 class="callout-title">Exercise 1: Replicates</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -1362,7 +1362,7 @@ <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>
@@ -1398,7 +1398,7 @@ <h3 class="callout-title">Exercise 2:</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -1412,7 +1412,7 @@ <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>
@@ -1540,7 +1540,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-19",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 78be4c9..69df603 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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 24eb82c..6aee044 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -413,7 +413,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index d4eb747..b1e6e15 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -867,7 +867,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-12",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 1340586..c5c2b61 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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index c5f7322..7bb551c 100644
--- a/large_data.html
+++ b/large_data.html
@@ -732,7 +732,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>From <code>?MulticoreParam</code> :</p>
 <blockquote>
@@ -937,7 +937,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>This code block calculates the exact PCA coordinates. Another thing
 to note: PC vectors are only identified up to a sign flip. We can see
@@ -1326,7 +1326,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1340,7 +1340,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb49">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1419,7 +1419,7 @@ <h3 class="callout-title">Exercise 2: Parallelization</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1432,7 +1432,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb55">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1554,7 +1554,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-26",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/multi-sample.html b/multi-sample.html
index d473983..772ccf9 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -535,7 +535,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -598,7 +598,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -1036,7 +1036,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. Rather than reporting e.g. a
 5-fold increase, it’s better to report a logFC of log(5) = 1.61.
@@ -1346,7 +1346,7 @@ <h3 class="callout-title">Exercise 1: Replicates</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Remember, you can subset SingleCellExperiments with logical indices,
 just like a matrix. You can also access their column data with the
@@ -1360,7 +1360,7 @@ <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>
@@ -1396,7 +1396,7 @@ <h3 class="callout-title">Exercise 2:</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>You can just hand <code>pheatmap()</code> a matrix as its only
 argument. It has a million options, but the defaults are usually pretty
@@ -1410,7 +1410,7 @@ <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>
@@ -1538,7 +1538,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-08-19",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 3825d74..e7499ed 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-27T01:14Z
+last_built: 2024-09-03T01:14Z
diff --git a/profiles.html b/profiles.html
index b6b6788..9106496 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": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 2f745a7..4fe2ab2 100644
--- a/reference.html
+++ b/reference.html
@@ -411,7 +411,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>