From d5edb9e6f259fc6235fef05346127ab636055e70 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 19 Apr 2024 21:11:04 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 98b79eba1eff68082e9c0d70a21a759282ab3922
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-04-19 21:10:41 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 40c788677f21dfb77104428e775c9d3e06a7c740
Branch  : main
Author  : lgeistlinger <ludwig.geistlinger@gmail.com>
Time    : 2024-04-19 20:31:54 +0000
Message : some cosmetics
---
 aio.html                             | 83 ++++++++++++++--------------
 cell_type_annotation.html            | 10 ++--
 hca.html                             | 36 ++++++------
 images.html                          |  2 +-
 instructor/aio.html                  | 83 ++++++++++++++--------------
 instructor/cell_type_annotation.html | 10 ++--
 instructor/hca.html                  | 36 ++++++------
 instructor/images.html               |  2 +-
 instructor/intro-sce.html            | 12 ++--
 instructor/large_data.html           | 25 ++++-----
 intro-sce.html                       | 12 ++--
 large_data.html                      | 25 ++++-----
 md5sum.txt                           |  6 +-
 pkgdown.yml                          |  2 +-
 14 files changed, 170 insertions(+), 174 deletions(-)

diff --git a/aio.html b/aio.html
index cd47a8c..be777f2 100644
--- a/aio.html
+++ b/aio.html
@@ -354,9 +354,9 @@ <h1 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a>
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"SummarizedExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"SingleCellExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"MouseGastrulationData"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="va">SummarizedExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">SingleCellExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">MouseGastrulationData</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">BiocStyle</span><span class="op">)</span></span></code></pre>
 </div>
 </div>
@@ -782,7 +782,7 @@ <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> function can be used to create
 a new SingleCellExperiment object</p>
@@ -795,7 +795,7 @@ <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>
@@ -823,7 +823,7 @@ <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" 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>
@@ -3228,7 +3228,7 @@ <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
@@ -3245,7 +3245,7 @@ <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>
@@ -3275,7 +3275,7 @@ <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/3.18/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3289,7 +3289,7 @@ <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>
@@ -3320,7 +3320,7 @@ <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>
@@ -4451,8 +4451,8 @@ <h3 class="card-title">Objectives</h3>
 computation.</li>
 <li>Learn how to invoke fast approximations for essential analysis
 steps.</li>
-<li>Learn how to convert SingleCellExperiment objects to SeuratObjects
-and AnnData objects.</li>
+<li>Learn how to convert <code>SingleCellExperiment</code> objects to
+<code>SeuratObject</code>s and <code>AnnData</code> objects.</li>
 </ul>
 </div>
 </div>
@@ -4861,21 +4861,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   2   0   0   0   1   0   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
    2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0   0
    4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 388   0   0   1   0   1   0   5   0   0   0
-   6    0   0   0   0   0 196  13   0   0   0   0   0   0   0   0
+   5    0   0   0   0 396   0   0   0   0   0   0   0   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   2   0   0   0   0
    7    0   0   0   0   0   0 245   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  96   0   0   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
    9    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 113   0   0   0   0   0
-   11   0   0   0   0   0   1   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   4   0   0   0   0  16   0 195   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
+   10   0   0   0   0   0   0   0   0   0 113 151   1   0   0   0
+   11   0   0   0   0   1   0   0   0   0   0   0 213   0   0   0
+   12   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -5538,7 +5537,7 @@ <h1 id="the-curatedatlasqueryr-project">The CuratedAtlasQueryR Project<a class="
 transcriptional profiles. This platform offers a standardized workflow
 for accessing atlas-level datasets programmatically and
 reproducibly.</p>
-<figure><img src="figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure>
+<figure><img src="figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure>
 </div>
 <div class="section level1">
 <h1 id="data-sources-in-r-bioconductor">Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a>
@@ -5699,9 +5698,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  3 ileum                           1
  4 transition zone of prostate     2
  5 peripheral zone of prostate     2
- 6 lymph node                      2
- 7 fovea centralis                 1
- 8 adrenal gland                   1
+ 6 fovea centralis                 1
+ 7 adrenal gland                   1
+ 8 lymph node                      2
  9 heart left ventricle            7
 10 bone marrow                     4
 # ℹ more rows</code></pre>
@@ -5740,16 +5739,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1018-azure:R 4.3.3/:memory:]
    assay                              n
    &lt;chr&gt;                          &lt;dbl&gt;
- 1 scRNA-seq                          4
- 2 Seq-Well                           2
- 3 Drop-seq                           1
- 4 10x 3' v3                         21
- 5 Slide-seq                          4
- 6 10x 3' v2                         27
- 7 Visium Spatial Gene Expression     7
- 8 10x 5' v2                          2
- 9 sci-RNA-seq                        1
-10 10x 3' v1                          1
+ 1 10x 5' v2                          2
+ 2 sci-RNA-seq                        1
+ 3 10x 3' v1                          1
+ 4 Smart-seq2                         1
+ 5 10x 3' v3                         21
+ 6 Slide-seq                          4
+ 7 10x 3' v2                         27
+ 8 Visium Spatial Gene Expression     7
+ 9 scRNA-seq                          4
+10 Seq-Well                           2
 # ℹ more rows</code></pre>
 </div>
 </div>
@@ -5953,7 +5952,7 @@ <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>
@@ -5987,7 +5986,7 @@ <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>
@@ -6021,7 +6020,7 @@ <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>
@@ -6063,7 +6062,7 @@ <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>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index a633a81..cd73139 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1348,7 +1348,7 @@ <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
@@ -1365,7 +1365,7 @@ <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>
@@ -1395,7 +1395,7 @@ <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/3.18/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1409,7 +1409,7 @@ <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>
@@ -1440,7 +1440,7 @@ <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>
diff --git a/hca.html b/hca.html
index 3fa3d76..150ef98 100644
--- a/hca.html
+++ b/hca.html
@@ -358,7 +358,7 @@ <h1 id="the-curatedatlasqueryr-project">The CuratedAtlasQueryR Project<a class="
 transcriptional profiles. This platform offers a standardized workflow
 for accessing atlas-level datasets programmatically and
 reproducibly.</p>
-<figure><img src="figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure></div>
+<figure><img src="figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure></div>
 <div class="section level1">
 <h1 id="data-sources-in-r-bioconductor">Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a></h1>
 <p>There are a few options to access single cell data with R /
@@ -495,9 +495,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  3 ileum                           1
  4 transition zone of prostate     2
  5 peripheral zone of prostate     2
- 6 lymph node                      2
- 7 fovea centralis                 1
- 8 adrenal gland                   1
+ 6 fovea centralis                 1
+ 7 adrenal gland                   1
+ 8 lymph node                      2
  9 heart left ventricle            7
 10 bone marrow                     4
 # ℹ more rows</code></pre>
@@ -534,16 +534,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1018-azure:R 4.3.3/:memory:]
    assay                              n
    &lt;chr&gt;                          &lt;dbl&gt;
- 1 scRNA-seq                          4
- 2 Seq-Well                           2
- 3 Drop-seq                           1
- 4 10x 3' v3                         21
- 5 Slide-seq                          4
- 6 10x 3' v2                         27
- 7 Visium Spatial Gene Expression     7
- 8 10x 5' v2                          2
- 9 sci-RNA-seq                        1
-10 10x 3' v1                          1
+ 1 10x 5' v2                          2
+ 2 sci-RNA-seq                        1
+ 3 10x 3' v1                          1
+ 4 Smart-seq2                         1
+ 5 10x 3' v3                         21
+ 6 Slide-seq                          4
+ 7 10x 3' v2                         27
+ 8 Visium Spatial Gene Expression     7
+ 9 scRNA-seq                          4
+10 Seq-Well                           2
 # ℹ more rows</code></pre>
 </div>
 </div>
@@ -738,7 +738,7 @@ <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">
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@@ -772,7 +772,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
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 </button>
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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@@ -848,7 +848,7 @@ <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">
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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diff --git a/images.html b/images.html
index d96c4d0..b009e78 100644
--- a/images.html
+++ b/images.html
@@ -382,7 +382,7 @@ <h3 id="multi-sample-figure-7">Figure 7</h3>
 <hr class="half-width"></section><section id="hca"><h2 class="section-heading"><a href="hca.html">Accessing data from the Human Cell Atlas (HCA)HCA Project<a class="anchor" aria-label="anchor" href="#hca-project"></a>CELLxGENE<a class="anchor" aria-label="anchor" href="#cellxgene"></a>CELLxGENE | Census<a class="anchor" aria-label="anchor" href="#cellxgene-census"></a>The CuratedAtlasQueryR Project<a class="anchor" aria-label="anchor" href="#the-curatedatlasqueryr-project"></a>Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a>Installation<a class="anchor" aria-label="anchor" href="#installation"></a>Package load<a class="anchor" aria-label="anchor" href="#package-load"></a>HCA Metadata<a class="anchor" aria-label="anchor" href="#hca-metadata"></a>A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a>Summarizing the metadata<a class="anchor" aria-label="anchor" href="#summarizing-the-metadata"></a>Columns available in the metadata<a class="anchor" aria-label="anchor" href="#columns-available-in-the-metadata"></a>Available assays<a class="anchor" aria-label="anchor" href="#available-assays"></a>Available organisms<a class="anchor" aria-label="anchor" href="#available-organisms"></a>Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a></a></h2>
 <hr class="half-width">
 <h3 id="hca-figure-1">Figure 1</h3>
-<figure><img src="figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure><hr></section>
 </div>
     </main>
 </div>
diff --git a/instructor/aio.html b/instructor/aio.html
index 348407c..1ddb538 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -357,9 +357,9 @@ <h1 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a>
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"SummarizedExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"SingleCellExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"MouseGastrulationData"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="va">SummarizedExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">SingleCellExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">MouseGastrulationData</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">BiocStyle</span><span class="op">)</span></span></code></pre>
 </div>
 </div>
@@ -785,7 +785,7 @@ <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> function can be used to create
 a new SingleCellExperiment object</p>
@@ -798,7 +798,7 @@ <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">
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 </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>
@@ -826,7 +826,7 @@ <h3 class="callout-title">Exercise 2<a class="anchor" aria-label="anchor" href="
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 </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>
@@ -3233,7 +3233,7 @@ <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
@@ -3250,7 +3250,7 @@ <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>
@@ -3280,7 +3280,7 @@ <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">
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 </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/3.18/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3294,7 +3294,7 @@ <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">
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 </button>
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 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3325,7 +3325,7 @@ <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">
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 <p>TODO</p>
 </div>
@@ -4458,8 +4458,8 @@ <h3 class="card-title">Objectives</h3>
 computation.</li>
 <li>Learn how to invoke fast approximations for essential analysis
 steps.</li>
-<li>Learn how to convert SingleCellExperiment objects to SeuratObjects
-and AnnData objects.</li>
+<li>Learn how to convert <code>SingleCellExperiment</code> objects to
+<code>SeuratObject</code>s and <code>AnnData</code> objects.</li>
 </ul>
 </div>
 </div>
@@ -4868,21 +4868,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   2   0   0   0   1   0   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
    2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0   0
    4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 388   0   0   1   0   1   0   5   0   0   0
-   6    0   0   0   0   0 196  13   0   0   0   0   0   0   0   0
+   5    0   0   0   0 396   0   0   0   0   0   0   0   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   2   0   0   0   0
    7    0   0   0   0   0   0 245   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  96   0   0   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
    9    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 113   0   0   0   0   0
-   11   0   0   0   0   0   1   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   4   0   0   0   0  16   0 195   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
+   10   0   0   0   0   0   0   0   0   0 113 151   1   0   0   0
+   11   0   0   0   0   1   0   0   0   0   0   0 213   0   0   0
+   12   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -5546,7 +5545,7 @@ <h1 id="the-curatedatlasqueryr-project">The CuratedAtlasQueryR Project<a class="
 transcriptional profiles. This platform offers a standardized workflow
 for accessing atlas-level datasets programmatically and
 reproducibly.</p>
-<figure><img src="../figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure>
+<figure><img src="../figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure>
 </div>
 <div class="section level1">
 <h1 id="data-sources-in-r-bioconductor">Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a>
@@ -5707,9 +5706,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  3 ileum                           1
  4 transition zone of prostate     2
  5 peripheral zone of prostate     2
- 6 lymph node                      2
- 7 fovea centralis                 1
- 8 adrenal gland                   1
+ 6 fovea centralis                 1
+ 7 adrenal gland                   1
+ 8 lymph node                      2
  9 heart left ventricle            7
 10 bone marrow                     4
 # ℹ more rows</code></pre>
@@ -5748,16 +5747,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1018-azure:R 4.3.3/:memory:]
    assay                              n
    &lt;chr&gt;                          &lt;dbl&gt;
- 1 scRNA-seq                          4
- 2 Seq-Well                           2
- 3 Drop-seq                           1
- 4 10x 3' v3                         21
- 5 Slide-seq                          4
- 6 10x 3' v2                         27
- 7 Visium Spatial Gene Expression     7
- 8 10x 5' v2                          2
- 9 sci-RNA-seq                        1
-10 10x 3' v1                          1
+ 1 10x 5' v2                          2
+ 2 sci-RNA-seq                        1
+ 3 10x 3' v1                          1
+ 4 Smart-seq2                         1
+ 5 10x 3' v3                         21
+ 6 Slide-seq                          4
+ 7 10x 3' v2                         27
+ 8 Visium Spatial Gene Expression     7
+ 9 scRNA-seq                          4
+10 Seq-Well                           2
 # ℹ more rows</code></pre>
 </div>
 </div>
@@ -5961,7 +5960,7 @@ <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>
@@ -5995,7 +5994,7 @@ <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">
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 </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">
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@@ -6029,7 +6028,7 @@ <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>
@@ -6071,7 +6070,7 @@ <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>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 15d7e69..a13c028 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -1350,7 +1350,7 @@ <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
@@ -1367,7 +1367,7 @@ <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>
@@ -1397,7 +1397,7 @@ <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/3.18/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1411,7 +1411,7 @@ <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>
@@ -1442,7 +1442,7 @@ <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>
diff --git a/instructor/hca.html b/instructor/hca.html
index 2e2fcdb..0527662 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -360,7 +360,7 @@ <h1 id="the-curatedatlasqueryr-project">The CuratedAtlasQueryR Project<a class="
 transcriptional profiles. This platform offers a standardized workflow
 for accessing atlas-level datasets programmatically and
 reproducibly.</p>
-<figure><img src="../figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure></div>
+<figure><img src="../figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure></div>
 <div class="section level1">
 <h1 id="data-sources-in-r-bioconductor">Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a></h1>
 <p>There are a few options to access single cell data with R /
@@ -497,9 +497,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  3 ileum                           1
  4 transition zone of prostate     2
  5 peripheral zone of prostate     2
- 6 lymph node                      2
- 7 fovea centralis                 1
- 8 adrenal gland                   1
+ 6 fovea centralis                 1
+ 7 adrenal gland                   1
+ 8 lymph node                      2
  9 heart left ventricle            7
 10 bone marrow                     4
 # ℹ more rows</code></pre>
@@ -536,16 +536,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 # Database: DuckDB v0.10.1 [unknown@Linux 6.5.0-1018-azure:R 4.3.3/:memory:]
    assay                              n
    &lt;chr&gt;                          &lt;dbl&gt;
- 1 scRNA-seq                          4
- 2 Seq-Well                           2
- 3 Drop-seq                           1
- 4 10x 3' v3                         21
- 5 Slide-seq                          4
- 6 10x 3' v2                         27
- 7 Visium Spatial Gene Expression     7
- 8 10x 5' v2                          2
- 9 sci-RNA-seq                        1
-10 10x 3' v1                          1
+ 1 10x 5' v2                          2
+ 2 sci-RNA-seq                        1
+ 3 10x 3' v1                          1
+ 4 Smart-seq2                         1
+ 5 10x 3' v3                         21
+ 6 Slide-seq                          4
+ 7 10x 3' v2                         27
+ 8 Visium Spatial Gene Expression     7
+ 9 scRNA-seq                          4
+10 Seq-Well                           2
 # ℹ more rows</code></pre>
 </div>
 </div>
@@ -740,7 +740,7 @@ <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>
@@ -774,7 +774,7 @@ <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>
@@ -808,7 +808,7 @@ <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>
@@ -850,7 +850,7 @@ <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>
diff --git a/instructor/images.html b/instructor/images.html
index c72bade..c79ad4b 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -384,7 +384,7 @@ <h3 id="multi-sample-figure-7">Figure 7</h3>
 <hr class="half-width"></section><section id="hca"><h2 class="section-heading"><a href="hca.html">Accessing data from the Human Cell Atlas (HCA)HCA Project<a class="anchor" aria-label="anchor" href="#hca-project"></a>CELLxGENE<a class="anchor" aria-label="anchor" href="#cellxgene"></a>CELLxGENE | Census<a class="anchor" aria-label="anchor" href="#cellxgene-census"></a>The CuratedAtlasQueryR Project<a class="anchor" aria-label="anchor" href="#the-curatedatlasqueryr-project"></a>Data Sources in R / Bioconductor<a class="anchor" aria-label="anchor" href="#data-sources-in-r-bioconductor"></a>Installation<a class="anchor" aria-label="anchor" href="#installation"></a>Package load<a class="anchor" aria-label="anchor" href="#package-load"></a>HCA Metadata<a class="anchor" aria-label="anchor" href="#hca-metadata"></a>A note on the piping operator<a class="anchor" aria-label="anchor" href="#a-note-on-the-piping-operator"></a>Summarizing the metadata<a class="anchor" aria-label="anchor" href="#summarizing-the-metadata"></a>Columns available in the metadata<a class="anchor" aria-label="anchor" href="#columns-available-in-the-metadata"></a>Available assays<a class="anchor" aria-label="anchor" href="#available-assays"></a>Available organisms<a class="anchor" aria-label="anchor" href="#available-organisms"></a>Exercises<a class="anchor" aria-label="anchor" href="#exercises"></a></a></h2>
 <hr class="half-width">
 <h3 id="hca-figure-1">Figure 1</h3>
-<figure><img src="../figures/HCA_sccomp_SUPPLEMENTARY_technical_cartoon_curatedAtlasQuery.png" class="figure mx-auto d-block"></figure><hr></section>
+<figure><img src="../figures/curatedAtlasQuery.png" class="figure mx-auto d-block"></figure><hr></section>
 </div>
     </main>
 </div>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 3580ed7..bff1c70 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -313,9 +313,9 @@ <h1 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a></h1
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"SummarizedExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"SingleCellExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"MouseGastrulationData"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="va">SummarizedExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">SingleCellExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">MouseGastrulationData</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">BiocStyle</span><span class="op">)</span></span></code></pre>
 </div>
 </div>
@@ -732,7 +732,7 @@ <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> function can be used to create
 a new SingleCellExperiment object</p>
@@ -745,7 +745,7 @@ <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>
@@ -773,7 +773,7 @@ <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" 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>
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 9853caf..3f281c9 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -305,8 +305,8 @@ <h3 class="card-title">Objectives</h3>
 computation.</li>
 <li>Learn how to invoke fast approximations for essential analysis
 steps.</li>
-<li>Learn how to convert SingleCellExperiment objects to SeuratObjects
-and AnnData objects.</li>
+<li>Learn how to convert <code>SingleCellExperiment</code> objects to
+<code>SeuratObject</code>s and <code>AnnData</code> objects.</li>
 </ul></div>
 </div>
 </div>
@@ -708,21 +708,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   2   0   0   0   1   0   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
    2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0   0
    4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 388   0   0   1   0   1   0   5   0   0   0
-   6    0   0   0   0   0 196  13   0   0   0   0   0   0   0   0
+   5    0   0   0   0 396   0   0   0   0   0   0   0   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   2   0   0   0   0
    7    0   0   0   0   0   0 245   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  96   0   0   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
    9    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 113   0   0   0   0   0
-   11   0   0   0   0   0   1   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   4   0   0   0   0  16   0 195   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
+   10   0   0   0   0   0   0   0   0   0 113 151   1   0   0   0
+   11   0   0   0   0   1   0   0   0   0   0   0 213   0   0   0
+   12   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
diff --git a/intro-sce.html b/intro-sce.html
index 958d475..65d62e6 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -311,9 +311,9 @@ <h1 id="setup">Setup<a class="anchor" aria-label="anchor" href="#setup"></a></h1
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="st">"SummarizedExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"SingleCellExperiment"</span><span class="op">)</span></span>
-<span><span class="kw">library</span><span class="op">(</span><span class="st">"MouseGastrulationData"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw">library</span><span class="op">(</span><span class="va">SummarizedExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">SingleCellExperiment</span><span class="op">)</span></span>
+<span><span class="kw">library</span><span class="op">(</span><span class="va">MouseGastrulationData</span><span class="op">)</span></span>
 <span><span class="kw">library</span><span class="op">(</span><span class="va">BiocStyle</span><span class="op">)</span></span></code></pre>
 </div>
 </div>
@@ -730,7 +730,7 @@ <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> function can be used to create
 a new SingleCellExperiment object</p>
@@ -743,7 +743,7 @@ <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>
@@ -771,7 +771,7 @@ <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" 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>
diff --git a/large_data.html b/large_data.html
index f110ae5..d8d76a4 100644
--- a/large_data.html
+++ b/large_data.html
@@ -303,8 +303,8 @@ <h3 class="card-title">Objectives</h3>
 computation.</li>
 <li>Learn how to invoke fast approximations for essential analysis
 steps.</li>
-<li>Learn how to convert SingleCellExperiment objects to SeuratObjects
-and AnnData objects.</li>
+<li>Learn how to convert <code>SingleCellExperiment</code> objects to
+<code>SeuratObject</code>s and <code>AnnData</code> objects.</li>
 </ul></div>
 </div>
 </div>
@@ -706,21 +706,20 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>     approx
 exact   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15
-   1   90   0   0   0   2   0   0   0   1   0   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
    2    0 143   0   0   0   0   0   0   0   0   0   0   0   0   1
-   3    0   0  75   0   0   0   0   0   0   0   0   0   0   0   0
+   3    0   0  77   0   0   0   0   0   0   0   0   0   0   0   0
    4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   0
-   5    0   0   0   0 388   0   0   1   0   1   0   5   0   0   0
-   6    0   0   0   0   0 196  13   0   0   0   0   0   0   0   0
+   5    0   0   0   0 396   0   0   0   0   0   0   0   0   0   0
+   6    0   0   0   0   0 210   0   0   0   0   2   0   0   0   0
    7    0   0   0   0   0   0 245   0   0   1   0   0   0   0   0
-   8    0   0   0   0   0   0   0  96   0   0   0   0   0   0   0
+   8    0   0   0   0   0   0   0  95   0   0   0   0   0   0   0
    9    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
-   10   0   0   0   0   0   0   0   0   0 113   0   0   0   0   0
-   11   0   0   0   0   0   1   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   4   0   0   0   0  16   0 195   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
+   10   0   0   0   0   0   0   0   0   0 113 151   1   0   0   0
+   11   0   0   0   0   1   0   0   0   0   0   0 213   0   0   0
+   12   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
+   13   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
+   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
diff --git a/md5sum.txt b/md5sum.txt
index 368b26a..933d907 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,12 +4,12 @@
 "config.yaml" "b0d664d3d6abdd0e98b16282e1c03107" "site/built/config.yaml" "2024-04-09"
 "index.md" "a02c9c785ed98ddd84fe3d34ddb12fcd" "site/built/index.md" "2024-04-09"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-04-09"
-"episodes/intro-sce.Rmd" "c051d0b936f6f6b4916e71e69033fc4f" "site/built/intro-sce.md" "2024-04-19"
+"episodes/intro-sce.Rmd" "dede7c455c15c681dcac9eed717d48a3" "site/built/intro-sce.md" "2024-04-19"
 "episodes/eda_qc.Rmd" "7ee0d6457a3d63e909a397a69732d07d" "site/built/eda_qc.md" "2024-04-09"
 "episodes/cell_type_annotation.Rmd" "8853c2680ab7e343e249f98ad4adfe26" "site/built/cell_type_annotation.md" "2024-04-09"
 "episodes/multi-sample.Rmd" "c95671a8765365f9802da9aedadf0e3a" "site/built/multi-sample.md" "2024-04-09"
-"episodes/large_data.Rmd" "0f78e3425dacf6d0c2098b4b50da415b" "site/built/large_data.md" "2024-04-19"
-"episodes/hca.Rmd" "3c404434b0c942a456f0e92e4311c046" "site/built/hca.md" "2024-04-19"
+"episodes/large_data.Rmd" "2735a12a1130dea13a98f4618f560ecc" "site/built/large_data.md" "2024-04-19"
+"episodes/hca.Rmd" "77d772ef05ed56e1cf5e8ffa147019ac" "site/built/hca.md" "2024-04-19"
 "instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-04-09"
 "learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-04-09"
 "learners/setup.md" "61568b36c8b96363218c9736f6aee03a" "site/built/setup.md" "2024-04-09"
diff --git a/pkgdown.yml b/pkgdown.yml
index b6d9cd6..9c68e8f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-04-19T19:06Z
+last_built: 2024-04-19T21:10Z