From 84aa90488bb8643b8e1fa7a8645fdf7e591b87dc Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 16 Jul 2024 01:05:08 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 8cd43889d9b38c2ac47c5eac089235832f63f893
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-09 00:36:05 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 480aa1aa5500cf810db82da76f40597b39ecf10c
Branch  : main
Author  : lgeistlinger <ludwig.geistlinger@gmail.com>
Time    : 2024-06-04 10:29:53 +0000
Message : Merge pull request #17 from ccb-hms/update/packages

Update 14 packages
---
 404.html                             |  4 ++--
 CODE_OF_CONDUCT.html                 |  2 +-
 LICENSE.html                         |  2 +-
 aio.html                             | 20 ++++++++++----------
 cell_type_annotation.html            | 12 ++++++------
 eda_qc.html                          |  6 +++---
 hca.html                             |  2 +-
 images.html                          |  4 ++--
 index.html                           |  4 ++--
 instructor-notes.html                |  4 ++--
 instructor/404.html                  |  4 ++--
 instructor/CODE_OF_CONDUCT.html      |  2 +-
 instructor/LICENSE.html              |  2 +-
 instructor/aio.html                  | 20 ++++++++++----------
 instructor/cell_type_annotation.html | 12 ++++++------
 instructor/eda_qc.html               |  6 +++---
 instructor/hca.html                  |  2 +-
 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, 79 insertions(+), 79 deletions(-)

diff --git a/404.html b/404.html
index 939ae09..a06065f 100644
--- a/404.html
+++ b/404.html
@@ -377,8 +377,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 22b95ce..cf014f5 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -399,7 +399,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index c75b731..bf9374f 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -450,7 +450,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 993ed2a..10e5bc5 100644
--- a/aio.html
+++ b/aio.html
@@ -819,7 +819,7 @@ <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" 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>
@@ -1067,7 +1067,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1881,7 +1881,7 @@ <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
@@ -3059,7 +3059,7 @@ <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3076,7 +3076,7 @@ <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" 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>TODO</p>
 </div>
@@ -3106,7 +3106,7 @@ <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" 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>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
@@ -3120,7 +3120,7 @@ <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" 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>TODO</p>
 </div>
@@ -3151,7 +3151,7 @@ <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" 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>TODO</p>
 </div>
@@ -6018,8 +6018,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index f5b9ed1..a506585 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1394,7 +1394,7 @@ <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1411,7 +1411,7 @@ <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" 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>TODO</p>
 </div>
@@ -1441,7 +1441,7 @@ <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" 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>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
@@ -1455,7 +1455,7 @@ <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" 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>TODO</p>
 </div>
@@ -1486,7 +1486,7 @@ <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" 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>TODO</p>
 </div>
@@ -1613,7 +1613,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index 3ac3139..e3c3c2a 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -509,7 +509,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1296,7 +1296,7 @@ <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
@@ -1450,7 +1450,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/hca.html b/hca.html
index 2e5caae..e64804c 100644
--- a/hca.html
+++ b/hca.html
@@ -1029,7 +1029,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index b6d22fb..df48b8b 100644
--- a/images.html
+++ b/images.html
@@ -488,8 +488,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index a59dd22..3628459 100644
--- a/index.html
+++ b/index.html
@@ -585,8 +585,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 0986f41..0b1ae0b 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -422,8 +422,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 6477984..cc41560 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -377,8 +377,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index e1e4258..fe85373 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -401,7 +401,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 0aa0c4e..09fd912 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -452,7 +452,7 @@ <h1>Licenses</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 7d41d7b..2eecc12 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -822,7 +822,7 @@ <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" 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>
@@ -1071,7 +1071,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1885,7 +1885,7 @@ <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
@@ -3064,7 +3064,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
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 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3081,7 +3081,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
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   <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>TODO</p>
 </div>
@@ -3111,7 +3111,7 @@ <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" 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>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
@@ -3125,7 +3125,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
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   <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>TODO</p>
 </div>
@@ -3156,7 +3156,7 @@ <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" 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>TODO</p>
 </div>
@@ -6026,8 +6026,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index fde458b..288573d 100644
--- a/instructor/cell_type_annotation.html
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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>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1413,7 +1413,7 @@ <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" 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>TODO</p>
 </div>
@@ -1443,7 +1443,7 @@ <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" 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>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
@@ -1457,7 +1457,7 @@ <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" 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>TODO</p>
 </div>
@@ -1488,7 +1488,7 @@ <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" 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>TODO</p>
 </div>
@@ -1615,7 +1615,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 29373d3..9305cd3 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -511,7 +511,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Setting the Random Seed </h3>
 </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
@@ -1298,7 +1298,7 @@ <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
@@ -1452,7 +1452,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/hca.html b/instructor/hca.html
index e50a78c..57310d2 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -1031,7 +1031,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 1fec2ff..b612b7c 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -490,8 +490,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 6b6c651..3de1b0d 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -669,8 +669,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index b6db5bc..60c1961 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -430,8 +430,8 @@ <h1>Instructor Notes</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/instructor-notes.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index b1bf3f5..608dd3b 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -770,7 +770,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
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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
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -890,7 +890,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 0243550..a436c5f 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -540,8 +540,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/instructor/large_data.html b/instructor/large_data.html
index 636d842..74f7146 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -1403,7 +1403,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 6614319..57ab7cb 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -1398,7 +1398,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index 7b9a5c4..460704b 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -352,8 +352,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 3b6db79..ec419c6 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -414,7 +414,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index 7d62b5a..52f2755 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -768,7 +768,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
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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
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -888,7 +888,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 035f1a8..d51db67 100644
--- a/key-points.html
+++ b/key-points.html
@@ -538,8 +538,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/large_data.html b/large_data.html
index 75a111f..66eb0ad 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1401,7 +1401,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>
diff --git a/multi-sample.html b/multi-sample.html
index cdf9367..acb6e58 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -1396,7 +1396,7 @@ <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": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
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   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index c451aec..5ccf4af 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
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+last_built: 2024-07-16T01:04Z
diff --git a/profiles.html b/profiles.html
index fe012f9..c8acbf1 100644
--- a/profiles.html
+++ b/profiles.html
@@ -352,8 +352,8 @@ <h1>Learner Profiles</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/profiles.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-16",
+  "datePublished": "2024-07-16"
 }
 
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diff --git a/reference.html b/reference.html
index 73e4744..2c04648 100644
--- a/reference.html
+++ b/reference.html
@@ -412,7 +412,7 @@ <h1>Reference</h1>
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-16"
 }
 
   </script><script>