From 0768439c82c80c8d993a3926c06d953811904e7d Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 8 Oct 2024 01:07:52 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 465803e8e8d894af4c7ce6b2121f0577eae3d5b3
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-10-07 19:23:59 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 2fa80f3351595c803ba1740e2827868e5de1b882
Branch  : main
Author  : Andrew Ghazi <6763470+andrewGhazi@users.noreply.github.com>
Time    : 2024-10-07 18:41:12 +0000
Message : Merge pull request #56 from ccb-hms/chimera_bg

background on chimera
---
 404.html                             |  4 +--
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE.html                         |  2 +-
 aio.html                             | 46 ++++++++++++++--------------
 cell_type_annotation.html            | 22 ++++++-------
 eda_qc.html                          | 24 +++++++--------
 hca.html                             |  2 +-
 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                  | 46 ++++++++++++++--------------
 instructor/cell_type_annotation.html | 22 ++++++-------
 instructor/eda_qc.html               | 24 +++++++--------
 instructor/hca.html                  |  2 +-
 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           |  2 +-
 instructor/multi-sample.html         |  2 +-
 instructor/profiles.html             |  4 +--
 instructor/reference.html            |  2 +-
 intro-sce.html                       |  2 +-
 key-points.html                      |  4 +--
 large_data.html                      |  2 +-
 multi-sample.html                    |  2 +-
 pkgdown.yml                          |  2 +-
 profiles.html                        |  4 +--
 reference.html                       |  2 +-
 33 files changed, 131 insertions(+), 131 deletions(-)

diff --git a/404.html b/404.html
index 09cbcde..962061c 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": "2024-10-07",
-  "datePublished": "2024-10-07"
+  "dateModified": "2024-10-08",
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index bd3821a..5edbc4f 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": "2024-09-24",
-  "datePublished": "2024-10-07"
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 40b3483..950a333 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": "2024-09-24",
-  "datePublished": "2024-10-07"
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 9aa787d..695236a 100644
--- a/aio.html
+++ b/aio.html
@@ -1171,7 +1171,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1253,7 +1253,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1479,7 +1479,7 @@ <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>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1755,7 +1755,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="cb42">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1871,7 +1871,7 @@ <h3 class="callout-title">Challenge</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><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1884,7 +1884,7 @@ <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">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -2100,7 +2100,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" 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="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2271,7 +2271,7 @@ <h3 class="callout-title">Exercise 1: Normalization</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb66">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2330,7 +2330,7 @@ <h3 class="callout-title">Exercise 2: PBMC Data</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>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2438,7 +2438,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2482,7 +2482,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -2756,7 +2756,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -2953,7 +2953,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -3251,7 +3251,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3515,7 +3515,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3665,7 +3665,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3682,7 +3682,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3721,7 +3721,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3794,7 +3794,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -3828,7 +3828,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -3870,7 +3870,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -7235,8 +7235,8 @@ <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": "2024-10-07",
-  "datePublished": "2024-10-07"
+  "dateModified": "2024-10-08",
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 1ec215c..9552ddb 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -516,7 +516,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -710,7 +710,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1005,7 +1005,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1268,7 +1268,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1413,7 +1413,7 @@ <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>
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 <p>The <code>NNGraphParam</code> constructor has an argument
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 <p>One important reason why is because averages over all other clusters
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@@ -1575,7 +1575,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
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 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
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@@ -1617,7 +1617,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
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 <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
@@ -1749,7 +1749,7 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/eda_qc.html b/eda_qc.html
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 </button>
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 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -797,7 +797,7 @@ <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">
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 <p>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1069,7 +1069,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 <p><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1194,7 +1194,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
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 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -1405,7 +1405,7 @@ <h3 class="callout-title">Challenge</h3>
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@@ -1569,7 +1569,7 @@ <h3 class="callout-title">Exercise 1: Normalization</h3>
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 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -1736,7 +1736,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
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 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
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 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
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   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
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 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1483,7 +1483,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
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 <p><code>modelGeneVar()</code> can take a <code>block</code>
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 <p>Use the <code>block</code> argument in the call to
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@@ -2104,7 +2104,7 @@ <h3 class="callout-title">Challenge</h3>
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@@ -2275,7 +2275,7 @@ <h3 class="callout-title">Exercise 1: Normalization</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb66">
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@@ -2334,7 +2334,7 @@ <h3 class="callout-title">Exercise 2: PBMC Data</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">
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 <div class="accordion-body">
 <p>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2442,7 +2442,7 @@ <h3 class="callout-title">Extension challenge 1: Spike-ins</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2486,7 +2486,7 @@ <h3 class="callout-title">Extension challenge 3: Reduced dimensionality represen
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
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 <div class="accordion-body">
 <p>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -2761,7 +2761,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <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
@@ -2958,7 +2958,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -3256,7 +3256,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3520,7 +3520,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3670,7 +3670,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3687,7 +3687,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3726,7 +3726,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
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@@ -3799,7 +3799,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -3833,7 +3833,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -3875,7 +3875,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -7243,8 +7243,8 @@ <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": "2024-10-07",
-  "datePublished": "2024-10-07"
+  "dateModified": "2024-10-08",
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index b3ff1b2..180e36b 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -518,7 +518,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>We see in the help documentation for <code>?clusterCells</code> that
 all of the clustering algorithm details are handled through the
@@ -712,7 +712,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>You can see that at least among the top markers, cluster 6 (pale
 green) tends to have the least separation from cluster 1.</p>
@@ -1007,7 +1007,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1270,7 +1270,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb43">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1415,7 +1415,7 @@ <h3 class="callout-title">Exercise 1: Clustering</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1432,7 +1432,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1470,7 +1470,7 @@ <h3 class="callout-title">Exercise 2: Reference marker genes</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb47">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1543,7 +1543,7 @@ <h3 class="callout-title">Extension Challenge 1: Group pair comparisons</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <p>One important reason why is because averages over all other clusters
 can be sensitive to the cell type composition. If a rare cell type shows
@@ -1577,7 +1577,7 @@ <h3 class="callout-title">Extension Challenge 2: Parallelizing SingleR</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <p>Use <code>BiocParallel</code> and the <code>BPPARAM</code> argument!
 This example will set it to use four cores on your laptop, but you can
@@ -1619,7 +1619,7 @@ <h3 class="callout-title">Extension Challenge 3: Critical inspection of diagnost
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <p>The example that jumps out most strongly to the eye is ExE endoderm,
 which doesn’t show clear separate modes. Simultaneously, Endothelium
@@ -1751,7 +1751,7 @@ <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": "2024-10-02",
-  "datePublished": "2024-10-07"
+  "datePublished": "2024-10-08"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 6954a68..dc15731 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -499,7 +499,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -580,7 +580,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -799,7 +799,7 @@ <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>You set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1071,7 +1071,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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="cb42">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1183,7 +1183,7 @@ <h3 class="callout-title">Challenge</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><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1196,7 +1196,7 @@ <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">
 <p>Use the <code>block</code> argument in the call to
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 <p>The first few lines here read the data from ExperimentHub and the
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 <p>Mathematically, this would require the data to fall on a
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