From 9d44a364f6fabd34d7622a3379343c375f62bac4 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 4 Jun 2024 00:37:16 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 9efcb0b7848459977e4d8d6c5a652d963022008c
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-05-29 00:17:43 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 9b877f37753f11bf472984ae6267e73dcc4d2127
Branch  : main
Author  : lgeistlinger <ludwig.geistlinger@gmail.com>
Time    : 2024-05-29 00:09:07 +0000
Message : Merge pull request #15 from ccb-hms/Citations

Added citations in footnote and ref page format
---
 404.html                             |  4 ++--
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE.html                         |  2 +-
 aio.html                             | 28 ++++++++++++++--------------
 cell_type_annotation.html            | 12 ++++++------
 eda_qc.html                          |  6 +++---
 hca.html                             | 10 +++++-----
 images.html                          |  4 ++--
 index.html                           |  4 ++--
 instructor-notes.html                |  4 ++--
 instructor/404.html                  |  4 ++--
 instructor/CODE_OF_CONDUCT.html      |  2 +-
 instructor/LICENSE.html              |  2 +-
 instructor/aio.html                  | 28 ++++++++++++++--------------
 instructor/cell_type_annotation.html | 12 ++++++------
 instructor/eda_qc.html               |  6 +++---
 instructor/hca.html                  | 10 +++++-----
 instructor/images.html               |  4 ++--
 instructor/index.html                |  4 ++--
 instructor/instructor-notes.html     |  4 ++--
 instructor/intro-sce.html            |  4 ++--
 instructor/key-points.html           |  4 ++--
 instructor/large_data.html           |  2 +-
 instructor/multi-sample.html         |  2 +-
 instructor/profiles.html             |  4 ++--
 instructor/reference.html            |  2 +-
 intro-sce.html                       |  4 ++--
 key-points.html                      |  4 ++--
 large_data.html                      |  2 +-
 multi-sample.html                    |  2 +-
 pkgdown.yml                          |  2 +-
 profiles.html                        |  4 ++--
 reference.html                       |  2 +-
 33 files changed, 95 insertions(+), 95 deletions(-)

diff --git a/404.html b/404.html
index 2a85c16..0ae40c5 100644
--- a/404.html
+++ b/404.html
@@ -324,8 +324,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 12b8074..39bf76c 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -346,7 +346,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 7852aa2..7dda612 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -397,7 +397,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index c53e0be..72ebd9e 100644
--- a/aio.html
+++ b/aio.html
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -1005,7 +1005,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1813,7 +1813,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -2983,7 +2983,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3000,7 +3000,7 @@ <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3030,7 +3030,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3044,7 +3044,7 @@ <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3075,7 +3075,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5688,7 +5688,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5722,7 +5722,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5756,7 +5756,7 @@ <h3 class="callout-title">Exercise 3<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5798,7 +5798,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5910,8 +5910,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index e4b04d1..ed861c4 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1341,7 +1341,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1358,7 +1358,7 @@ <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1388,7 +1388,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1402,7 +1402,7 @@ <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1433,7 +1433,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1560,7 +1560,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index d7d0113..0edb16f 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -457,7 +457,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1244,7 +1244,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1398,7 +1398,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/hca.html b/hca.html
index d3ff49f..6645056 100644
--- a/hca.html
+++ b/hca.html
@@ -744,7 +744,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -778,7 +778,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -812,7 +812,7 @@ <h3 class="callout-title">Exercise 3<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -854,7 +854,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -976,7 +976,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 04764df..96b6db7 100644
--- a/images.html
+++ b/images.html
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diff --git a/index.html b/index.html
index b913422..b8aaf1d 100644
--- a/index.html
+++ b/index.html
@@ -522,8 +522,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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-  "dateModified": "2024-05-29",
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 }
 
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diff --git a/instructor-notes.html b/instructor-notes.html
index c2bc3ef..84c393f 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -364,8 +364,8 @@ <h1>Instructor Notes</h1>
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-  "dateModified": "2024-05-29",
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 }
 
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diff --git a/instructor/404.html b/instructor/404.html
index 8648e5e..14f7187 100644
--- a/instructor/404.html
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-  "dateModified": "2024-05-29",
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 }
 
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 0ac1166..f336bee 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -348,7 +348,7 @@ <h1>Contributor Code of Conduct</h1>
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index a766520..d24049f 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -399,7 +399,7 @@ <h1>Licenses</h1>
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diff --git a/instructor/aio.html b/instructor/aio.html
index f064f18..464f60c 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -761,7 +761,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
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 </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
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-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1817,7 +1817,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
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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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
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@@ -3005,7 +3005,7 @@ <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="accordion-body">
 <p>TODO</p>
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@@ -3035,7 +3035,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
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-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
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 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3049,7 +3049,7 @@ <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
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-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3080,7 +3080,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
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-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <p>TODO</p>
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 <div class="accordion-body">
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 <div class="codewrapper sourceCode" id="cb25">
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 <div class="codewrapper sourceCode" id="cb26">
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@@ -5806,7 +5806,7 @@ <h3 class="callout-title">Exercise 4<a class="anchor" aria-label="anchor" href="
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <div class="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>
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diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index bad4336..4db20fd 100644
--- a/instructor/cell_type_annotation.html
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 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
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@@ -1360,7 +1360,7 @@ <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
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+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1390,7 +1390,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
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   <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1404,7 +1404,7 @@ <h4 class="accordion-header" id="headingHint2">Give me a hint</h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1435,7 +1435,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1562,7 +1562,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index bb5ea0d..0c6cb6f 100644
--- a/instructor/eda_qc.html
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@@ -459,7 +459,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
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 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1246,7 +1246,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1400,7 +1400,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
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diff --git a/instructor/hca.html b/instructor/hca.html
index 9ffc778..2939ac3 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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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>
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-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="codewrapper sourceCode" id="cb26">
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-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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diff --git a/instructor/images.html b/instructor/images.html
index ca37da6..e9adeff 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -432,8 +432,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 33c0e76..dcbf79a 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -606,8 +606,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index ca840bd..82266e5 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -372,8 +372,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 1ff021e..c48ea6b 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -717,7 +717,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -837,7 +837,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 55f5604..8475ff7 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -482,8 +482,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 437f24e..4b20974 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -1346,7 +1346,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index d3d2925..67a09b3 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -1345,7 +1345,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index b8208a7..bfa1ac3 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -299,8 +299,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 8f03239..c6fab33 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -361,7 +361,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index 26ce334..29fe37e 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -715,7 +715,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -835,7 +835,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index d6d570f..86a3e2c 100644
--- a/key-points.html
+++ b/key-points.html
@@ -480,8 +480,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index 0b0c685..1ea66b0 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1344,7 +1344,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/multi-sample.html b/multi-sample.html
index a775b10..739fb66 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -1343,7 +1343,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-23",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 89a4672..def32d0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-29T00:20Z
+last_built: 2024-06-04T00:36Z
 
diff --git a/profiles.html b/profiles.html
index ad72117..c08e3d8 100644
--- a/profiles.html
+++ b/profiles.html
@@ -299,8 +299,8 @@ <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": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "dateModified": "2024-06-04",
+  "datePublished": "2024-06-04"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index b29b39b..88e4f15 100644
--- a/reference.html
+++ b/reference.html
@@ -359,7 +359,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-05-29",
-  "datePublished": "2024-05-29"
+  "datePublished": "2024-06-04"
 }
 
   </script><script>