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--- a/404.html
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-  "dateModified": "2024-10-11",
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diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 11ee5c7..ccb6201 100644
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diff --git a/LICENSE.html b/LICENSE.html
index e066b3e..42f5b99 100644
--- a/LICENSE.html
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   "dateCreated": "2024-01-10",
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diff --git a/aio.html b/aio.html
index 7abdffb..faf599e 100644
--- a/aio.html
+++ b/aio.html
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 <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" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -627,7 +627,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -775,7 +775,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -855,7 +855,7 @@ <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
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 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
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@@ -868,7 +868,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
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@@ -921,7 +921,7 @@ <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" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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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>
@@ -4204,7 +4204,7 @@ <h3 class="callout-title">Challenge</h3>
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
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 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
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@@ -4269,7 +4269,7 @@ <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>
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 <div class="accordion-body">
 <p>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -4722,7 +4722,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -5048,7 +5048,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</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>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -5062,7 +5062,7 @@ <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">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5097,7 +5097,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -5112,7 +5112,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5195,7 +5195,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</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">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -7276,8 +7276,8 @@ <h3 class="callout-title">Key Points</h3>
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-  "dateModified": "2024-10-11",
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diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index b164d1b..424c2c5 100644
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index 44e16c7..0a18861 100644
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diff --git a/hca.html b/hca.html
index 33022cc..e1aa7a3 100644
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diff --git a/images.html b/images.html
index 97d51fe..27622ab 100644
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diff --git a/index.html b/index.html
index b312825..7bfa9a6 100644
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diff --git a/instructor-notes.html b/instructor-notes.html
index 61d611f..0cbced9 100644
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diff --git a/instructor/404.html b/instructor/404.html
index 4cecda5..40b4322 100644
--- a/instructor/404.html
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   "dateCreated": "2024-01-10",
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 7ce42f3..efd3fe7 100644
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 2f0dab6..295fcf5 100644
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diff --git a/instructor/aio.html b/instructor/aio.html
index deb4f40..543ae00 100644
--- a/instructor/aio.html
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 <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" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -630,7 +630,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -778,7 +778,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -858,7 +858,7 @@ <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">
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-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
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 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
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@@ -871,7 +871,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -924,7 +924,7 @@ <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" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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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>
@@ -4210,7 +4210,7 @@ <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>
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-<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>Samples 5 and 6 were from the same “pool” of cells. Looking at the
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 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
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@@ -5054,7 +5054,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
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 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
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@@ -5068,7 +5068,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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@@ -5103,7 +5103,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
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 <p>After running the second pseudobulk DGE, you can join the two
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@@ -5118,7 +5118,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
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@@ -5201,7 +5201,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</h3>
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 <div class="accordion-body">
 <p>It’s important to have multiple samples within each experimental
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@@ -7284,8 +7284,8 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
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diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index f95a6ec..5ed3ea8 100644
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diff --git a/instructor/hca.html b/instructor/hca.html
index 4c76cb9..4da4796 100644
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diff --git a/instructor/images.html b/instructor/images.html
index 2ac7165..3e13d9e 100644
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diff --git a/instructor/index.html b/instructor/index.html
index 59f84e0..feafcef 100644
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 612db2d..2125349 100644
--- a/instructor/instructor-notes.html
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 }
 
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diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 48c3042..fac28b6 100644
--- a/instructor/intro-sce.html
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   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Benefits of using the integrated SingleCellExperiment data container </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
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@@ -579,7 +579,7 @@ <h3 class="callout-title">Challenge</h3>
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 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -724,7 +724,7 @@ <h3 class="callout-title">Challenge</h3>
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 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
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 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
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diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 13afdee..23ecb6a 100644
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
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 <div class="accordion-body">
 <p>Samples 5 and 6 were from the same “pool” of cells. Looking at the
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@@ -608,7 +608,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>False. Batch-level data can be retained through confounding with
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@@ -1057,7 +1057,7 @@ <h3 class="callout-title">Challenge</h3>
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 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
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@@ -1374,7 +1374,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</h3>
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 <p>You can simply hand <code>pheatmap()</code> a matrix as its only
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@@ -1388,7 +1388,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
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 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1423,7 +1423,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
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 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1438,7 +1438,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
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   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
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+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1521,7 +1521,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</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">
 <p>It’s important to have multiple samples within each experimental
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@@ -1650,7 +1650,7 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index 9f7732d..db7681a 100644
--- a/instructor/profiles.html
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index a19f405..4bf23e2 100644
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+++ b/instructor/reference.html
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-09-24",
-  "datePublished": "2024-10-11"
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index 51f38a5..f170460 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -496,7 +496,7 @@ <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" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>The complexity of the <code>SingleCellExperiment</code> container
 might be a little bit intimidating in the beginning. One might be
@@ -577,7 +577,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Here we obtain the sixth sample and assign it to
 <code>sce6</code>:</p>
@@ -722,7 +722,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>Here, we add a column named <code>conservation</code> that could
 represent an evolutionary conservation score.</p>
@@ -801,7 +801,7 @@ <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" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -814,7 +814,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -867,7 +867,7 @@ <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" 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="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -998,7 +998,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-10-11"
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 115f5b8..e6e10bf 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": "2024-10-11",
-  "datePublished": "2024-10-11"
+  "dateModified": "2024-10-15",
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index fbd6ec4..bc10d21 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": "2024-10-07",
-  "datePublished": "2024-10-11"
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/multi-sample.html b/multi-sample.html
index 2473052..ee98c32 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -543,7 +543,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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>Samples 5 and 6 were from the same “pool” of cells. Looking at the
 documentation for the dataset under <code>?WTChimeraData</code> we see
@@ -606,7 +606,7 @@ <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>False. Batch-level data can be retained through confounding with
 experimental factors or poor ability to distinguish experimental effects
@@ -1055,7 +1055,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>“logFC” stands for log fold-change. <code>edgeR</code> uses a log2
 convention. Rather than reporting e.g. a 5-fold increase, it’s better to
@@ -1372,7 +1372,7 @@ <h3 class="callout-title">Exercise 1: Heatmaps</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>You can simply hand <code>pheatmap()</code> a matrix as its only
 argument. <code>pheatmap()</code> has a million options you can tweak,
@@ -1386,7 +1386,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb52">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1421,7 +1421,7 @@ <h3 class="callout-title">Exercise 2: Model specification and comparison</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>After running the second pseudobulk DGE, you can join the two
 <code>DataFrame</code>s of <code>Erythroid3</code> statistics using the
@@ -1436,7 +1436,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" 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="cb53">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1519,7 +1519,7 @@ <h3 class="callout-title">Extension challenge 1: Group effects</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">
 <p>It’s important to have multiple samples within each experimental
 group because it helps the batch effect correction algorithm distinguish
@@ -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": "2024-10-11"
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index d4be6c1..f99c803 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-11T19:44Z
+last_built: 2024-10-15T01:11Z
diff --git a/profiles.html b/profiles.html
index 642a102..40e9d10 100644
--- a/profiles.html
+++ b/profiles.html
@@ -374,8 +374,8 @@ <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": "2024-10-11",
-  "datePublished": "2024-10-11"
+  "dateModified": "2024-10-15",
+  "datePublished": "2024-10-15"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 0c09826..4e2fff1 100644
--- a/reference.html
+++ b/reference.html
@@ -411,7 +411,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-09-24",
-  "datePublished": "2024-10-11"
+  "datePublished": "2024-10-15"
 }
 
   </script><script>