diff --git a/404.html b/404.html
index 179b287..09cbcde 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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 3d063ad..bd3821a 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": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 17e9ce8..40b3483 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": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 581f8aa..f8325a9 100644
--- a/aio.html
+++ b/aio.html
@@ -544,7 +544,7 @@ <h3 id="motivation-and-overview">Motivation and overview<a class="anchor" aria-l
 <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> Benefits of using the integrated SingleCellExperiment data container </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -622,7 +622,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -770,7 +770,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -850,7 +850,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -863,7 +863,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -916,7 +916,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1159,7 +1159,7 @@ <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">
 <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>
@@ -1241,7 +1241,7 @@ <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" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <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
@@ -1467,7 +1467,7 @@ <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 set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1743,7 +1743,7 @@ <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" 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="cb42">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1859,7 +1859,7 @@ <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" 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><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1872,7 +1872,7 @@ <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -2088,7 +2088,7 @@ <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" 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="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2259,7 +2259,7 @@ <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" 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="cb66">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2318,7 +2318,7 @@ <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" 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>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2426,7 +2426,7 @@ <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" 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>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2470,7 +2470,7 @@ <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" 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>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -6931,7 +6931,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6982,7 +6982,7 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7023,7 +7023,7 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7115,7 +7115,7 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb31">
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@@ -7224,8 +7224,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 7d15de7..2445313 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1749,7 +1749,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-02",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index a378a95..6d6c9af 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -497,7 +497,7 @@ <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">
 <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>
@@ -578,7 +578,7 @@ <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" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <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">
   <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 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
 <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="cb42">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1181,7 +1181,7 @@ <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" 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><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>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>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>
 <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="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1569,7 +1569,7 @@ <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" 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="cb66">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1628,7 +1628,7 @@ <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" 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>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>
 <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>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -1780,7 +1780,7 @@ <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" 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>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -1919,7 +1919,7 @@ <h3 class="callout-title">Further Reading</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-03",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/hca.html b/hca.html
index f53511d..37dfb6a 100644
--- a/hca.html
+++ b/hca.html
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -809,7 +809,7 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -850,7 +850,7 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -942,7 +942,7 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1064,7 +1064,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 3c25e47..28d2726 100644
--- a/images.html
+++ b/images.html
@@ -510,8 +510,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 66a1500..d9ddbbf 100644
--- a/index.html
+++ b/index.html
@@ -365,164 +365,14 @@ <h3 id="r-and-rstudio">R and RStudio<a class="anchor" aria-label="anchor" href="
 <ul><li>R and RStudio are separate downloads and installations. R is a
 programming language and collection of software that implements that
 language. RStudio is a graphical integrated development environment
-(IDE) that makes using R much easier and more interactive. You need to
+(IDE) that makes using R easier and more interactive. You need to
 install R before you install RStudio. After installing both programs,
-you will need to install some R libraries from within RStudio. Follow
-the instructions below for your operating system, and then follow the
-instructions to install packages.</li>
+you will need to install some R libraries from within RStudio. If you
+need to install R and/or RStudio, there are platform-specific
+installation instructions in the <a href="https://carpentries-incubator.github.io/bioc-intro/" class="external-link">Introduction
+to Bioconductor module</a>.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="you-are-running-windows">You are running Windows<a class="anchor" aria-label="anchor" href="#you-are-running-windows"></a></h3>
-<p><br></p>
-<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you already have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
-<div class="accordion-body">
-<ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
-version is available, quit RStudio, and download the latest version for
-RStudio.</li>
-<li>To check which version of R you are using, start RStudio and the
-first thing that appears in the console indicates the version of R you
-are running. Alternatively, you can type <code>sessionInfo()</code>,
-which will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/windows/base/" class="external-link">CRAN website</a> and
-check whether a more recent version is available. If so, please download
-and install it. You can <a href="https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f" class="external-link">check
-here</a> for more information on how to remove old versions from your
-system if you wish to do so.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you don’t have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
-<div class="accordion-body">
-<ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
-website</a>.</li>
-<li>Run the <code>.exe</code> file that was just downloaded</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select <strong>RStudio
-xxxx.yy.zz-uuu.exe - Windows 10/11</strong> (where x, y, z, and u
-represent version numbers)</li>
-<li>Double click the file to install it</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
-<h3 id="you-are-running-macos">You are running macOS<a class="anchor" aria-label="anchor" href="#you-are-running-macos"></a></h3>
-<p><br></p>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you already have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
-<div class="accordion-body">
-<ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
-version is available, quit RStudio, and download the latest version for
-RStudio.</li>
-<li>To check the version of R you are using, start RStudio and the first
-thing that appears on the terminal indicates the version of R you are
-running. Alternatively, you can type <code>sessionInfo()</code>, which
-will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a> and check
-whether a more recent version is available. If so, please download and
-install it.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you don’t have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
-<div class="accordion-body">
-<ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
-<li>Select the <code>.pkg</code> file for the latest R version</li>
-<li>Double click on the downloaded file to install R</li>
-<li>It is also a good idea to install <a href="https://www.xquartz.org/" class="external-link">XQuartz</a> (needed by some
-packages)</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select <strong>RStudio
-xxxx.yy.zz-uuu.dmg - macOS 10.15+</strong> (where x, y, z, and u
-represent version numbers)</li>
-<li>Double click the file to install RStudio</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
-<h3 id="you-are-running-linux">You are running Linux<a class="anchor" aria-label="anchor" href="#you-are-running-linux"></a></h3>
-<p><br></p>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  Install R using your package manager and RStudio
-  </h4>
-</button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
-<div class="accordion-body">
-<ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
-information to get the most recent version of R for common
-distributions. For most distributions, you could use your package
-manager (e.g., for Debian/Ubuntu run
-<code>sudo apt-get install r-base</code>, and for Fedora
-<code>sudo yum install R</code>), but we don’t recommend this approach
-as the versions provided by this are usually out of date. In any case,
-make sure you have at least R 4.2.0.</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select the version that matches your
-distribution, and install it with your preferred method (e.g., with
-Debian/Ubuntu <code>sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb</code>
-at the terminal).</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages.</li>
-<li>Follow the steps in the <a href="#for-everyone">instructions for
-everyone</a>
-</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
 <h3 id="for-everyone">For everyone<a class="anchor" aria-label="anchor" href="#for-everyone"></a></h3>
 <p>After installing R and RStudio, you need to install some packages
 that will be used during the workshop. We will also learn about package
@@ -535,32 +385,18 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">install.packages</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"BiocManager"</span>, <span class="st">"remotes"</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"AUCell"</span>, <span class="st">"batchelor"</span>, <span class="st">"BiocNeighbors"</span>, </span>
-<span>                       <span class="st">"BiocParallel"</span>, <span class="st">"BiocSingular"</span>, <span class="st">"BiocStyle"</span>, </span>
-<span>                       <span class="st">"bluster"</span>, <span class="st">"CuratedAtlasQueryR"</span>, <span class="st">"dplyr"</span>, </span>
-<span>                       <span class="st">"DropletUtils"</span>, <span class="st">"edgeR"</span>, <span class="st">"EnsDb.Mmusculus.v79"</span>, </span>
-<span>                       <span class="st">"ggplot2"</span>, <span class="st">"GSEABase"</span>, <span class="st">"MouseGastrulationData"</span>,</span>
-<span>                       <span class="st">"pheatmap"</span>, <span class="st">"scater"</span>, <span class="st">"scDblFinder"</span>, <span class="st">"scran"</span>, </span>
-<span>                       <span class="st">"scuttle"</span>, <span class="st">"Seurat"</span>, <span class="st">"SeuratData"</span>, </span>
-<span>                       <span class="st">"SingleCellExperiment"</span>, <span class="st">"SingleR"</span>,</span>
-<span>                       <span class="st">"TENxBrainData"</span>, <span class="st">"zellkonverter"</span><span class="op">)</span>,</span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"AUCell"</span>, <span class="st">"batchelor"</span>, <span class="st">"BiocStyle"</span>, </span>
+<span>                       <span class="st">"CuratedAtlasQueryR"</span>, <span class="st">"DropletUtils"</span>, </span>
+<span>                       <span class="st">"EnsDb.Mmusculus.v79"</span>, <span class="st">"MouseGastrulationData"</span>,</span>
+<span>                       <span class="st">"scDblFinder"</span>, <span class="st">"Seurat"</span>, <span class="st">"lgeistlinger/SeuratData"</span>,</span>
+<span>                       <span class="st">"SingleR"</span>, <span class="st">"TENxBrainData"</span>, <span class="st">"zellkonverter"</span><span class="op">)</span>,</span>
 <span>                       Ncpus <span class="op">=</span> <span class="fl">4</span><span class="op">)</span></span></code></pre>
 </div>
 <!---
 grep -Ph "library\(" episodes/*.Rmd | sort | uniq
 
-^these are all libraries used in the episodes
+^these are all libraries loaded in the episodes
 -->
-<p>On the off chance your computer don’t have multiple CPU cores, remove
-the <code>Ncpus = 4</code> argument.</p>
-<p>If you’ve worked with Bioconductor packages before, and the
-installation command offers to update packages that have newer versions,
-saying something like:</p>
-<pre><code>&lt;...long list of packages...&gt;
-
-Update all/some/none? [a/s/n]:</code></pre>
-<p>Select <code>n</code> for no. If old packages turn out to be a
-problem, cross that bridge when you come to it.</p>
 <!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
@@ -617,8 +453,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index d2a9e6a..de485be 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -433,8 +433,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index efd19dd..0aed455 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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 34c9f39..016b4c7 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -401,7 +401,7 @@ <h1>Contributor Code of Conduct</h1>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-09-24",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 9685e4e..45438d1 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": "2024-09-24",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
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diff --git a/instructor/aio.html b/instructor/aio.html
index 345c2f9..d8c9714 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -547,7 +547,7 @@ <h3 id="motivation-and-overview">Motivation and overview<a class="anchor" aria-l
 <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> Benefits of using the integrated SingleCellExperiment data container </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -625,7 +625,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -773,7 +773,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -853,7 +853,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -866,7 +866,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -919,7 +919,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1163,7 +1163,7 @@ <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">
 <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>
@@ -1245,7 +1245,7 @@ <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" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <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
@@ -1471,7 +1471,7 @@ <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 set <code>nmads = 4</code> like so:</p>
 <div class="codewrapper sourceCode" id="cb24">
@@ -1747,7 +1747,7 @@ <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" 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="cb42">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1863,7 +1863,7 @@ <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" 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><code>modelGeneVar()</code> can take a <code>block</code>
 argument.</p>
@@ -1876,7 +1876,7 @@ <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -2092,7 +2092,7 @@ <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" 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="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2263,7 +2263,7 @@ <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" 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="cb66">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2322,7 +2322,7 @@ <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" 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>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -2430,7 +2430,7 @@ <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" 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>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -2474,7 +2474,7 @@ <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" 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>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -6939,7 +6939,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6990,7 +6990,7 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7031,7 +7031,7 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7123,7 +7123,7 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7232,8 +7232,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index ea91a94..14ded2f 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -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": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 28c6a89..6954a68 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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="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" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <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" 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 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" 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="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" 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><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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Use the <code>block</code> argument in the call to
 <code>modelGeneVar()</code> like so:</p>
@@ -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="#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="cb56">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1571,7 +1571,7 @@ <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" 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="cb66">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1630,7 +1630,7 @@ <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" 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>The first few lines here read the data from ExperimentHub and the
 mitochondrial genes are identified by gene symbols in the row data.
@@ -1738,7 +1738,7 @@ <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" 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>Spike-ins are deliberately-introduced exogeneous RNA from an exotic
 or synthetic source at a known concentration. This provides a known
@@ -1782,7 +1782,7 @@ <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" 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>Mathematically, this would require the data to fall on a
 two-dimensional plane (for linear methods like PCA) or a smooth 2D
@@ -1921,7 +1921,7 @@ <h3 class="callout-title">Further Reading</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-03",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/hca.html b/instructor/hca.html
index baf6094..5a5b8ac 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -760,7 +760,7 @@ <h3 class="callout-title">Exercise 1: Basic counting + piping</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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="cb23">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -811,7 +811,7 @@ <h3 class="callout-title">Exercise 2: Tissue &amp; type counting</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -852,7 +852,7 @@ <h3 class="callout-title">Exercise 3: Comparing metadata categories</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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">
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@@ -944,7 +944,7 @@ <h3 class="callout-title">Exercise 4: Highly specific cell groups</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" 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="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1066,7 +1066,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 961e047..3b780fc 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -512,8 +512,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 67da909..de15da4 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -450,164 +450,14 @@ <h3 id="r-and-rstudio">R and RStudio<a class="anchor" aria-label="anchor" href="
 <ul><li>R and RStudio are separate downloads and installations. R is a
 programming language and collection of software that implements that
 language. RStudio is a graphical integrated development environment
-(IDE) that makes using R much easier and more interactive. You need to
+(IDE) that makes using R easier and more interactive. You need to
 install R before you install RStudio. After installing both programs,
-you will need to install some R libraries from within RStudio. Follow
-the instructions below for your operating system, and then follow the
-instructions to install packages.</li>
+you will need to install some R libraries from within RStudio. If you
+need to install R and/or RStudio, there are platform-specific
+installation instructions in the <a href="https://carpentries-incubator.github.io/bioc-intro/" class="external-link">Introduction
+to Bioconductor module</a>.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="you-are-running-windows">You are running Windows<a class="anchor" aria-label="anchor" href="#you-are-running-windows"></a></h3>
-<p><br></p>
-<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you already have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
-<div class="accordion-body">
-<ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
-version is available, quit RStudio, and download the latest version for
-RStudio.</li>
-<li>To check which version of R you are using, start RStudio and the
-first thing that appears in the console indicates the version of R you
-are running. Alternatively, you can type <code>sessionInfo()</code>,
-which will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/windows/base/" class="external-link">CRAN website</a> and
-check whether a more recent version is available. If so, please download
-and install it. You can <a href="https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f" class="external-link">check
-here</a> for more information on how to remove old versions from your
-system if you wish to do so.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you don’t have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
-<div class="accordion-body">
-<ul><li>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
-website</a>.</li>
-<li>Run the <code>.exe</code> file that was just downloaded</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select <strong>RStudio
-xxxx.yy.zz-uuu.exe - Windows 10/11</strong> (where x, y, z, and u
-represent version numbers)</li>
-<li>Double click the file to install it</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
-<h3 id="you-are-running-macos">You are running macOS<a class="anchor" aria-label="anchor" href="#you-are-running-macos"></a></h3>
-<p><br></p>
-<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you already have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
-<div class="accordion-body">
-<ul><li>Open RStudio, and click on “Help” &gt; “Check for updates”. If a new
-version is available, quit RStudio, and download the latest version for
-RStudio.</li>
-<li>To check the version of R you are using, start RStudio and the first
-thing that appears on the terminal indicates the version of R you are
-running. Alternatively, you can type <code>sessionInfo()</code>, which
-will also display which version of R you are running. Go on the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a> and check
-whether a more recent version is available. If so, please download and
-install it.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  If you don’t have R and RStudio installed
-  </h4>
-</button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
-<div class="accordion-body">
-<ul><li>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</li>
-<li>Select the <code>.pkg</code> file for the latest R version</li>
-<li>Double click on the downloaded file to install R</li>
-<li>It is also a good idea to install <a href="https://www.xquartz.org/" class="external-link">XQuartz</a> (needed by some
-packages)</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select <strong>RStudio
-xxxx.yy.zz-uuu.dmg - macOS 10.15+</strong> (where x, y, z, and u
-represent version numbers)</li>
-<li>Double click the file to install RStudio</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages.</li>
-<li>Follow the steps in the instructions <a href="#for-everyone">for
-everyone</a> at the bottom of this page.</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
-<h3 id="you-are-running-linux">You are running Linux<a class="anchor" aria-label="anchor" href="#you-are-running-linux"></a></h3>
-<p><br></p>
-<div id="accordionSolution5" class="accordion challenge-accordion accordion-flush">
-<div class="accordion-item">
-<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">
-  Install R using your package manager and RStudio
-  </h4>
-</button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
-<div class="accordion-body">
-<ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
-information to get the most recent version of R for common
-distributions. For most distributions, you could use your package
-manager (e.g., for Debian/Ubuntu run
-<code>sudo apt-get install r-base</code>, and for Fedora
-<code>sudo yum install R</code>), but we don’t recommend this approach
-as the versions provided by this are usually out of date. In any case,
-make sure you have at least R 4.2.0.</li>
-<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download" class="external-link">RStudio
-download page</a>
-</li>
-<li>Under <em>All Installers</em> select the version that matches your
-distribution, and install it with your preferred method (e.g., with
-Debian/Ubuntu <code>sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb</code>
-at the terminal).</li>
-<li>Once it’s installed, open RStudio to make sure it works and you
-don’t get any error messages.</li>
-<li>Follow the steps in the <a href="#for-everyone">instructions for
-everyone</a>
-</li>
-</ul></div>
-</div>
-</div>
-</div>
-</div>
-<div class="section level3">
 <h3 id="for-everyone">For everyone<a class="anchor" aria-label="anchor" href="#for-everyone"></a></h3>
 <p>After installing R and RStudio, you need to install some packages
 that will be used during the workshop. We will also learn about package
@@ -620,32 +470,18 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">install.packages</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"BiocManager"</span>, <span class="st">"remotes"</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"AUCell"</span>, <span class="st">"batchelor"</span>, <span class="st">"BiocNeighbors"</span>, </span>
-<span>                       <span class="st">"BiocParallel"</span>, <span class="st">"BiocSingular"</span>, <span class="st">"BiocStyle"</span>, </span>
-<span>                       <span class="st">"bluster"</span>, <span class="st">"CuratedAtlasQueryR"</span>, <span class="st">"dplyr"</span>, </span>
-<span>                       <span class="st">"DropletUtils"</span>, <span class="st">"edgeR"</span>, <span class="st">"EnsDb.Mmusculus.v79"</span>, </span>
-<span>                       <span class="st">"ggplot2"</span>, <span class="st">"GSEABase"</span>, <span class="st">"MouseGastrulationData"</span>,</span>
-<span>                       <span class="st">"pheatmap"</span>, <span class="st">"scater"</span>, <span class="st">"scDblFinder"</span>, <span class="st">"scran"</span>, </span>
-<span>                       <span class="st">"scuttle"</span>, <span class="st">"Seurat"</span>, <span class="st">"SeuratData"</span>, </span>
-<span>                       <span class="st">"SingleCellExperiment"</span>, <span class="st">"SingleR"</span>,</span>
-<span>                       <span class="st">"TENxBrainData"</span>, <span class="st">"zellkonverter"</span><span class="op">)</span>,</span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="fu">c</span><span class="op">(</span><span class="st">"AUCell"</span>, <span class="st">"batchelor"</span>, <span class="st">"BiocStyle"</span>, </span>
+<span>                       <span class="st">"CuratedAtlasQueryR"</span>, <span class="st">"DropletUtils"</span>, </span>
+<span>                       <span class="st">"EnsDb.Mmusculus.v79"</span>, <span class="st">"MouseGastrulationData"</span>,</span>
+<span>                       <span class="st">"scDblFinder"</span>, <span class="st">"Seurat"</span>, <span class="st">"lgeistlinger/SeuratData"</span>,</span>
+<span>                       <span class="st">"SingleR"</span>, <span class="st">"TENxBrainData"</span>, <span class="st">"zellkonverter"</span><span class="op">)</span>,</span>
 <span>                       Ncpus <span class="op">=</span> <span class="fl">4</span><span class="op">)</span></span></code></pre>
 </div>
 <!---
 grep -Ph "library\(" episodes/*.Rmd | sort | uniq
 
-^these are all libraries used in the episodes
+^these are all libraries loaded in the episodes
 -->
-<p>On the off chance your computer don’t have multiple CPU cores, remove
-the <code>Ncpus = 4</code> argument.</p>
-<p>If you’ve worked with Bioconductor packages before, and the
-installation command offers to update packages that have newer versions,
-saying something like:</p>
-<pre><code>&lt;...long list of packages...&gt;
-
-Update all/some/none? [a/s/n]:</code></pre>
-<p>Select <code>n</code> for no. If old packages turn out to be a
-problem, cross that bridge when you come to it.</p>
 <!--
 Place links that you need to refer to multiple times across pages here. Delete
 any links that you are not going to use.
@@ -702,8 +538,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index ca23ba6..350b9a9 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -441,8 +441,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 8412fcf..95b566a 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -497,7 +497,7 @@ <h3 id="motivation-and-overview">Motivation and overview<a class="anchor" aria-l
 <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> Benefits of using the integrated SingleCellExperiment data container </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -573,7 +573,7 @@ <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">
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 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
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@@ -718,7 +718,7 @@ <h3 class="callout-title">Challenge</h3>
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   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
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-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
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   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
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@@ -810,7 +810,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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   <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">
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 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -863,7 +863,7 @@ <h3 class="callout-title">Exercise 2</h3>
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   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
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-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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@@ -991,7 +991,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index 273d466..7469efd 100644
--- a/instructor/key-points.html
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@@ -540,8 +540,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
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diff --git a/instructor/large_data.html b/instructor/large_data.html
index bc68f9d..c13098f 100644
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+++ b/instructor/large_data.html
@@ -1610,7 +1610,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
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diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 92d94d5..d5880b3 100644
--- a/instructor/multi-sample.html
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@@ -1650,7 +1650,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index 48677b4..426b8b1 100644
--- a/instructor/profiles.html
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   "dateCreated": "2024-01-10",
-  "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
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diff --git a/instructor/reference.html b/instructor/reference.html
index 85f4c33..036e4dc 100644
--- a/instructor/reference.html
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-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
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diff --git a/intro-sce.html b/intro-sce.html
index e149192..c5efb0e 100644
--- a/intro-sce.html
+++ b/intro-sce.html
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 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
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@@ -571,7 +571,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -716,7 +716,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -795,7 +795,7 @@ <h3 class="callout-title">Exercise 1</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -808,7 +808,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -861,7 +861,7 @@ <h3 class="callout-title">Exercise 2</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -989,7 +989,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 4894366..845ba7e 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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
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diff --git a/large_data.html b/large_data.html
index 64130c5..a9bd7a2 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1608,7 +1608,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
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diff --git a/md5sum.txt b/md5sum.txt
index d2023bb..9de0485 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -12,6 +12,6 @@
 "episodes/hca.Rmd" "1577de2f4a851c7e99e3a8459230d6f1" "site/built/hca.md" "2024-10-04"
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 "learners/reference.md" "40fc1d0be2412d2d9d434a5bc84e4de8" "site/built/reference.md" "2024-09-24"
-"learners/setup.md" "688e3116d23d078822c9977961d8c1ae" "site/built/setup.md" "2024-10-04"
+"learners/setup.md" "3e40ed251636d7ae77a69cf37724d6e5" "site/built/setup.md" "2024-10-07"
 "profiles/learner-profiles.md" "074074346a544b8d2e0774998781c5d4" "site/built/learner-profiles.md" "2024-09-24"
 "renv/profiles/lesson-requirements/renv.lock" "615a211004ad17d22300cc9cab7c6e38" "site/built/renv.lock" "2024-09-24"
diff --git a/multi-sample.html b/multi-sample.html
index a642ecf..e65d5b3 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -1648,7 +1648,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
 }
 
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diff --git a/pkgdown.yml b/pkgdown.yml
index 682b1fc..868ef4c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-04T23:51Z
+last_built: 2024-10-07T17:27Z
diff --git a/profiles.html b/profiles.html
index 61f9e82..4e62344 100644
--- a/profiles.html
+++ b/profiles.html
@@ -370,8 +370,8 @@ <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": "2024-10-04",
-  "datePublished": "2024-10-04"
+  "dateModified": "2024-10-07",
+  "datePublished": "2024-10-07"
 }
 
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diff --git a/reference.html b/reference.html
index 9b3ac60..8da564d 100644
--- a/reference.html
+++ b/reference.html
@@ -411,7 +411,7 @@ <h1>Reference</h1>
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-09-24",
-  "datePublished": "2024-10-04"
+  "datePublished": "2024-10-07"
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