diff --git a/404.html b/404.html
index 25476ce..e14b0e9 100644
--- a/404.html
+++ b/404.html
@@ -355,7 +355,7 @@ <h1>Page not found</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
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diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 39c365d..8415057 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -376,7 +376,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -398,8 +398,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 091a4e9..81e53d9 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -427,7 +427,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -449,8 +449,8 @@ <h1>Licenses</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/LICENSE.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 0c77b3a..7590b70 100644
--- a/aio.html
+++ b/aio.html
@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -816,7 +816,7 @@ <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>
@@ -883,7 +883,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1970,7 +1970,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </ol>
 </div></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/cell_type_annotation.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2917,7 +2917,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -2974,16 +2974,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [35] RSQLite_2.3.7             beachmat_2.20.0          
  [37] labeling_0.4.3            filelock_1.0.3           
  [39] fansi_1.0.6               httr_1.4.7               
- [41] abind_1.4-5               compiler_4.4.0           
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  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
  [47] DBI_1.2.3                 highr_0.11               
  [49] R.utils_2.12.3            MASS_7.3-60.2            
  [51] rappdirs_0.3.3            DelayedArray_0.30.1      
- [53] rjson_0.2.21              tools_4.4.0              
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  [55] vipor_0.4.7               beeswarm_0.4.0           
  [57] R.oo_1.26.0               glue_1.7.0               
- [59] nlme_3.1-164              grid_4.4.0               
+ [59] nlme_3.1-164              grid_4.4.1               
  [61] cluster_2.1.6             generics_0.1.3           
  [63] gtable_0.3.5              R.methodsS3_1.8.2        
  [65] tidyr_1.3.1               data.table_1.15.4        
@@ -2992,7 +2992,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [71] XVector_0.44.0            ggrepel_0.9.5            
  [73] BiocVersion_3.19.1        pillar_1.9.0             
  [75] limma_3.60.2              BumpyMatrix_1.12.0       
- [77] splines_4.4.0             dplyr_1.1.4              
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  [79] BiocFileCache_2.12.0      lattice_0.22-6           
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
@@ -3008,7 +3008,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [103] uwot_0.2.2                xtable_1.8-4             
 [105] segmented_2.1-0           munsell_0.5.1            
 [107] Rcpp_1.0.12               dbplyr_2.5.0             
-[109] png_0.1-8                 parallel_4.4.0           
+[109] png_0.1-8                 parallel_4.4.1           
 [111] blob_1.2.4                sparseMatrixStats_1.16.0 
 [113] viridisLite_0.4.2         scales_1.3.0             
 [115] purrr_1.0.2               crayon_1.5.2             
@@ -3040,7 +3040,7 @@ <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
@@ -3057,7 +3057,7 @@ <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>
@@ -3087,7 +3087,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3101,7 +3101,7 @@ <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>
@@ -3132,7 +3132,7 @@ <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>
@@ -3206,7 +3206,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-multi-sample"><p>Content from <a href="multi-sample.html">Multi-sample analyses</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/multi-sample.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -4006,7 +4006,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -4042,7 +4042,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
   [1] DBI_1.2.3                 formatR_1.14             
   [3] gridExtra_2.3             rlang_1.1.3              
-  [5] magrittr_2.0.3            compiler_4.4.0           
+  [5] magrittr_2.0.3            compiler_4.4.1           
   [7] RSQLite_2.3.7             DelayedMatrixStats_1.26.0
   [9] png_0.1-8                 vctrs_0.6.5              
  [11] pkgconfig_2.0.3           crayon_1.5.2             
@@ -4057,9 +4057,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [29] jsonlite_1.8.8            blob_1.2.4               
  [31] highr_0.11                DelayedArray_0.30.1      
  [33] BiocParallel_1.38.0       cluster_2.1.6            
- [35] irlba_2.3.5.1             parallel_4.4.0           
+ [35] irlba_2.3.5.1             parallel_4.4.1           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.47                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.1            
  [41] igraph_2.0.3              Matrix_1.7-0             
  [43] tidyselect_1.2.1          viridis_0.6.5            
  [45] abind_1.4-5               yaml_2.3.8               
@@ -4074,10 +4074,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [63] generics_0.1.3            BiocVersion_3.19.1       
  [65] sparseMatrixStats_1.16.0  munsell_0.5.1            
  [67] scales_1.3.0              glue_1.7.0               
- [69] metapod_1.12.0            tools_4.4.0              
+ [69] metapod_1.12.0            tools_4.4.1              
  [71] AnnotationHub_3.12.0      BiocNeighbors_1.22.0     
  [73] ScaledMatrix_1.12.0       locfit_1.5-9.9           
- [75] cowplot_1.1.3             grid_4.4.0               
+ [75] cowplot_1.1.3             grid_4.4.1               
  [77] AnnotationDbi_1.66.0      colorspace_2.1-0         
  [79] GenomeInfoDbData_1.2.12   beeswarm_0.4.0           
  [81] BiocSingular_1.20.0       vipor_0.4.7              
@@ -4115,7 +4115,7 @@ <h3 class="callout-title">Exercise 1: Replicates<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">
 
 </div>
@@ -4127,7 +4127,7 @@ <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>
@@ -4152,7 +4152,7 @@ <h3 class="callout-title">Exercise 2: <code>muscat</code><a class="anchor" aria-
 <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">
 
 </div>
@@ -4164,7 +4164,7 @@ <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>
@@ -4230,7 +4230,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -4668,21 +4668,20 @@ <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   0   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 203   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0 395   0   1   0   0   1   0   1   0   0   0
-   6    0   0   0   0   0  81 127   0   0   0   1   0   0   0   0
+   1   90   0   0   0   1   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  77   0   1   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 342   0   0   0   0   0   0   0   0   0   0  55
+   5    0   0   0   0  90   0   0  95   0   0   0   8   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
    7    0   0   0   0   0 245   0   0   0   1   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   4  10   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 143   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0   0   0 203   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   6   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  51   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   8    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
+   9    0   0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0   5 142   0   6   0   0
+   11   0   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0 303   0   0   0   0   0   0   0   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</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4962,7 +4961,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -5004,7 +5003,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
   [1] RcppAnnoy_0.0.22          later_1.3.2              
-  [3] splines_4.4.0             filelock_1.0.3           
+  [3] splines_4.4.1             filelock_1.0.3           
   [5] tibble_3.2.1              polyclip_1.10-6          
   [7] basilisk.utils_1.16.0     fastDummies_1.7.3        
   [9] lifecycle_1.0.4           edgeR_4.2.0              
@@ -5031,7 +5030,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] viridis_0.6.5             spatstat.explore_3.2-7   
  [53] BiocFileCache_2.12.0      jsonlite_1.8.8           
  [55] progressr_0.14.0          ggridges_0.5.6           
- [57] survival_3.6-4            tools_4.4.0              
+ [57] survival_3.6-4            tools_4.4.1              
  [59] ica_1.0-3                 Rcpp_1.0.12              
  [61] glue_1.7.0                gridExtra_2.3            
  [63] xfun_0.44                 dplyr_1.1.4              
@@ -5056,16 +5055,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
 [105] BiocVersion_3.19.1        KernSmooth_2.23-24       
-[107] parallel_4.4.0            miniUI_0.1.1.1           
+[107] parallel_4.4.1            miniUI_0.1.1.1           
 [109] vipor_0.4.7               AnnotationDbi_1.66.0     
-[111] pillar_1.9.0              grid_4.4.0               
+[111] pillar_1.9.0              grid_4.4.1               
 [113] vctrs_0.6.5               RANN_2.6.1               
 [115] promises_1.3.0            dbplyr_2.5.0             
 [117] beachmat_2.20.0           xtable_1.8-4             
 [119] cluster_2.1.6             beeswarm_0.4.0           
 [121] evaluate_0.23             magick_2.8.3             
 [123] cli_3.6.2                 locfit_1.5-9.9           
-[125] compiler_4.4.0            rlang_1.1.3              
+[125] compiler_4.4.1            rlang_1.1.3              
 [127] crayon_1.5.2              future.apply_1.11.2      
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
@@ -5104,7 +5103,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <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>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5118,7 +5117,7 @@ <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>
@@ -5146,7 +5145,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <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 function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5159,7 +5158,7 @@ <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>
@@ -5189,7 +5188,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5201,7 +5200,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5257,7 +5256,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 any links that you are not going to use. 
  --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -5949,7 +5948,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -5972,8 +5971,8 @@ <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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 65eae3f..85aeac5 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Cell type annotation</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/cell_type_annotation.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1272,7 +1272,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1329,16 +1329,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [35] RSQLite_2.3.7             beachmat_2.20.0          
  [37] labeling_0.4.3            filelock_1.0.3           
  [39] fansi_1.0.6               httr_1.4.7               
- [41] abind_1.4-5               compiler_4.4.0           
+ [41] abind_1.4-5               compiler_4.4.1           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
  [47] DBI_1.2.3                 highr_0.11               
  [49] R.utils_2.12.3            MASS_7.3-60.2            
  [51] rappdirs_0.3.3            DelayedArray_0.30.1      
- [53] rjson_0.2.21              tools_4.4.0              
+ [53] rjson_0.2.21              tools_4.4.1              
  [55] vipor_0.4.7               beeswarm_0.4.0           
  [57] R.oo_1.26.0               glue_1.7.0               
- [59] nlme_3.1-164              grid_4.4.0               
+ [59] nlme_3.1-164              grid_4.4.1               
  [61] cluster_2.1.6             generics_0.1.3           
  [63] gtable_0.3.5              R.methodsS3_1.8.2        
  [65] tidyr_1.3.1               data.table_1.15.4        
@@ -1347,7 +1347,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [71] XVector_0.44.0            ggrepel_0.9.5            
  [73] BiocVersion_3.19.1        pillar_1.9.0             
  [75] limma_3.60.2              BumpyMatrix_1.12.0       
- [77] splines_4.4.0             dplyr_1.1.4              
+ [77] splines_4.4.1             dplyr_1.1.4              
  [79] BiocFileCache_2.12.0      lattice_0.22-6           
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
@@ -1363,7 +1363,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [103] uwot_0.2.2                xtable_1.8-4             
 [105] segmented_2.1-0           munsell_0.5.1            
 [107] Rcpp_1.0.12               dbplyr_2.5.0             
-[109] png_0.1-8                 parallel_4.4.0           
+[109] png_0.1-8                 parallel_4.4.1           
 [111] blob_1.2.4                sparseMatrixStats_1.16.0 
 [113] viridisLite_0.4.2         scales_1.3.0             
 [115] purrr_1.0.2               crayon_1.5.2             
@@ -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" 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
@@ -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" 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>
@@ -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" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -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" 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>
@@ -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" 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>
@@ -1590,7 +1590,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1612,8 +1612,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/eda_qc.html b/eda_qc.html
index 7cc8b9b..3215e2a 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory data analysis and quality control</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1427,7 +1427,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 		</footer></div> <!-- / div.container -->
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@@ -1449,8 +1449,8 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
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 }
 
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diff --git a/hca.html b/hca.html
index 4c366b2..79ac8bd 100644
--- a/hca.html
+++ b/hca.html
@@ -339,7 +339,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Accessing data from the Human Cell Atlas (HCA)</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
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@@ -1006,7 +1006,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 	<div id="to-top">
@@ -1028,8 +1028,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
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diff --git a/images.html b/images.html
index 0a3f0d5..9592d3b 100644
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -488,8 +488,8 @@ <h3 id="hca-figure-1">Figure 1</h3>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/images.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-25",
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 }
 
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diff --git a/index.html b/index.html
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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-<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">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</p></li>
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-<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">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
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@@ -453,7 +453,7 @@ <h4 class="accordion-header" id="headingSolution4">
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   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</p></li>
 <li><p>Select the <code>.pkg</code> file for the latest R
@@ -486,7 +486,7 @@ <h4 class="accordion-header" id="headingSolution5">
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
@@ -563,7 +563,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
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-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -585,8 +585,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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diff --git a/instructor-notes.html b/instructor-notes.html
index 642d63c..56c70be 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -399,7 +399,7 @@ <h1>Instructor Notes</h1>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -422,8 +422,8 @@ <h1>Instructor Notes</h1>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor-notes.html",
   "dateCreated": "2024-01-10",
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diff --git a/instructor/404.html b/instructor/404.html
index 9af0385..611f2cd 100644
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 		</footer></div> <!-- / div.container -->
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@@ -377,8 +377,8 @@ <h1>Page not found</h1>
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   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/404.html",
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 }
 
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 0d8c5e7..75c5cc9 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -378,7 +378,7 @@ <h1>Contributor Code of Conduct</h1>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -400,8 +400,8 @@ <h1>Contributor Code of Conduct</h1>
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   "dateCreated": "2024-01-10",
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diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 8af97d9..094b75d 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
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@@ -429,7 +429,7 @@ <h1>Licenses</h1>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 		</footer></div> <!-- / div.container -->
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@@ -451,8 +451,8 @@ <h1>Licenses</h1>
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diff --git a/instructor/aio.html b/instructor/aio.html
index c6d24a1..52a8467 100644
--- a/instructor/aio.html
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@@ -370,7 +370,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -819,7 +819,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
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+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
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 </section></section><section id="aio-eda_qc"><p>Content from <a href="eda_qc.html">Exploratory data analysis and quality control</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -1974,7 +1974,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
 </ol>
 </div></section><section id="aio-cell_type_annotation"><p>Content from <a href="cell_type_annotation.html">Cell type annotation</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/cell_type_annotation.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -2922,7 +2922,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -2979,16 +2979,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [35] RSQLite_2.3.7             beachmat_2.20.0          
  [37] labeling_0.4.3            filelock_1.0.3           
  [39] fansi_1.0.6               httr_1.4.7               
- [41] abind_1.4-5               compiler_4.4.0           
+ [41] abind_1.4-5               compiler_4.4.1           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
  [47] DBI_1.2.3                 highr_0.11               
  [49] R.utils_2.12.3            MASS_7.3-60.2            
  [51] rappdirs_0.3.3            DelayedArray_0.30.1      
- [53] rjson_0.2.21              tools_4.4.0              
+ [53] rjson_0.2.21              tools_4.4.1              
  [55] vipor_0.4.7               beeswarm_0.4.0           
  [57] R.oo_1.26.0               glue_1.7.0               
- [59] nlme_3.1-164              grid_4.4.0               
+ [59] nlme_3.1-164              grid_4.4.1               
  [61] cluster_2.1.6             generics_0.1.3           
  [63] gtable_0.3.5              R.methodsS3_1.8.2        
  [65] tidyr_1.3.1               data.table_1.15.4        
@@ -2997,7 +2997,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [71] XVector_0.44.0            ggrepel_0.9.5            
  [73] BiocVersion_3.19.1        pillar_1.9.0             
  [75] limma_3.60.2              BumpyMatrix_1.12.0       
- [77] splines_4.4.0             dplyr_1.1.4              
+ [77] splines_4.4.1             dplyr_1.1.4              
  [79] BiocFileCache_2.12.0      lattice_0.22-6           
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
@@ -3013,7 +3013,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [103] uwot_0.2.2                xtable_1.8-4             
 [105] segmented_2.1-0           munsell_0.5.1            
 [107] Rcpp_1.0.12               dbplyr_2.5.0             
-[109] png_0.1-8                 parallel_4.4.0           
+[109] png_0.1-8                 parallel_4.4.1           
 [111] blob_1.2.4                sparseMatrixStats_1.16.0 
 [113] viridisLite_0.4.2         scales_1.3.0             
 [115] purrr_1.0.2               crayon_1.5.2             
@@ -3045,7 +3045,7 @@ <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
@@ -3062,7 +3062,7 @@ <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>
@@ -3092,7 +3092,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3106,7 +3106,7 @@ <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>
@@ -3137,7 +3137,7 @@ <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>
@@ -3211,7 +3211,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-multi-sample"><p>Content from <a href="multi-sample.html">Multi-sample analyses</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/multi-sample.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -4012,7 +4012,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -4048,7 +4048,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
   [1] DBI_1.2.3                 formatR_1.14             
   [3] gridExtra_2.3             rlang_1.1.3              
-  [5] magrittr_2.0.3            compiler_4.4.0           
+  [5] magrittr_2.0.3            compiler_4.4.1           
   [7] RSQLite_2.3.7             DelayedMatrixStats_1.26.0
   [9] png_0.1-8                 vctrs_0.6.5              
  [11] pkgconfig_2.0.3           crayon_1.5.2             
@@ -4063,9 +4063,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [29] jsonlite_1.8.8            blob_1.2.4               
  [31] highr_0.11                DelayedArray_0.30.1      
  [33] BiocParallel_1.38.0       cluster_2.1.6            
- [35] irlba_2.3.5.1             parallel_4.4.0           
+ [35] irlba_2.3.5.1             parallel_4.4.1           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.47                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.1            
  [41] igraph_2.0.3              Matrix_1.7-0             
  [43] tidyselect_1.2.1          viridis_0.6.5            
  [45] abind_1.4-5               yaml_2.3.8               
@@ -4080,10 +4080,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [63] generics_0.1.3            BiocVersion_3.19.1       
  [65] sparseMatrixStats_1.16.0  munsell_0.5.1            
  [67] scales_1.3.0              glue_1.7.0               
- [69] metapod_1.12.0            tools_4.4.0              
+ [69] metapod_1.12.0            tools_4.4.1              
  [71] AnnotationHub_3.12.0      BiocNeighbors_1.22.0     
  [73] ScaledMatrix_1.12.0       locfit_1.5-9.9           
- [75] cowplot_1.1.3             grid_4.4.0               
+ [75] cowplot_1.1.3             grid_4.4.1               
  [77] AnnotationDbi_1.66.0      colorspace_2.1-0         
  [79] GenomeInfoDbData_1.2.12   beeswarm_0.4.0           
  [81] BiocSingular_1.20.0       vipor_0.4.7              
@@ -4121,7 +4121,7 @@ <h3 class="callout-title">Exercise 1: Replicates<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">
 
 </div>
@@ -4133,7 +4133,7 @@ <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>
@@ -4158,7 +4158,7 @@ <h3 class="callout-title">Exercise 2: <code>muscat</code><a class="anchor" aria-
 <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">
 
 </div>
@@ -4170,7 +4170,7 @@ <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>
@@ -4236,7 +4236,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-large_data"><p>Content from <a href="large_data.html">Working with large data</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
@@ -4675,21 +4675,20 @@ <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   0   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 203   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0 395   0   1   0   0   1   0   1   0   0   0
-   6    0   0   0   0   0  81 127   0   0   0   1   0   0   0   0
+   1   90   0   0   0   1   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  77   0   1   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 342   0   0   0   0   0   0   0   0   0   0  55
+   5    0   0   0   0  90   0   0  95   0   0   0   8   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
    7    0   0   0   0   0 245   0   0   0   1   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   4  10   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 143   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0   0   0 203   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   6   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  51   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   8    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
+   9    0   0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0   5 142   0   6   0   0
+   11   0   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0 303   0   0   0   0   0   0   0   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</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4969,7 +4968,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -5011,7 +5010,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
   [1] RcppAnnoy_0.0.22          later_1.3.2              
-  [3] splines_4.4.0             filelock_1.0.3           
+  [3] splines_4.4.1             filelock_1.0.3           
   [5] tibble_3.2.1              polyclip_1.10-6          
   [7] basilisk.utils_1.16.0     fastDummies_1.7.3        
   [9] lifecycle_1.0.4           edgeR_4.2.0              
@@ -5038,7 +5037,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] viridis_0.6.5             spatstat.explore_3.2-7   
  [53] BiocFileCache_2.12.0      jsonlite_1.8.8           
  [55] progressr_0.14.0          ggridges_0.5.6           
- [57] survival_3.6-4            tools_4.4.0              
+ [57] survival_3.6-4            tools_4.4.1              
  [59] ica_1.0-3                 Rcpp_1.0.12              
  [61] glue_1.7.0                gridExtra_2.3            
  [63] xfun_0.44                 dplyr_1.1.4              
@@ -5063,16 +5062,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
 [105] BiocVersion_3.19.1        KernSmooth_2.23-24       
-[107] parallel_4.4.0            miniUI_0.1.1.1           
+[107] parallel_4.4.1            miniUI_0.1.1.1           
 [109] vipor_0.4.7               AnnotationDbi_1.66.0     
-[111] pillar_1.9.0              grid_4.4.0               
+[111] pillar_1.9.0              grid_4.4.1               
 [113] vctrs_0.6.5               RANN_2.6.1               
 [115] promises_1.3.0            dbplyr_2.5.0             
 [117] beachmat_2.20.0           xtable_1.8-4             
 [119] cluster_2.1.6             beeswarm_0.4.0           
 [121] evaluate_0.23             magick_2.8.3             
 [123] cli_3.6.2                 locfit_1.5-9.9           
-[125] compiler_4.4.0            rlang_1.1.3              
+[125] compiler_4.4.1            rlang_1.1.3              
 [127] crayon_1.5.2              future.apply_1.11.2      
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
@@ -5111,7 +5110,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <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>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5125,7 +5124,7 @@ <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>
@@ -5153,7 +5152,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <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 function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5166,7 +5165,7 @@ <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>
@@ -5196,7 +5195,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5208,7 +5207,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5264,7 +5263,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 any links that you are not going to use. 
  --></section></section><section id="aio-hca"><p>Content from <a href="hca.html">Accessing data from the Human Cell Atlas (HCA)</a></p>
 <hr>
-<p>Last updated on 2024-06-04 |
+<p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -5957,7 +5956,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -5980,8 +5979,8 @@ <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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 482e7a7..250745e 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Cell type annotation</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/cell_type_annotation.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1274,7 +1274,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1331,16 +1331,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [35] RSQLite_2.3.7             beachmat_2.20.0          
  [37] labeling_0.4.3            filelock_1.0.3           
  [39] fansi_1.0.6               httr_1.4.7               
- [41] abind_1.4-5               compiler_4.4.0           
+ [41] abind_1.4-5               compiler_4.4.1           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
  [47] DBI_1.2.3                 highr_0.11               
  [49] R.utils_2.12.3            MASS_7.3-60.2            
  [51] rappdirs_0.3.3            DelayedArray_0.30.1      
- [53] rjson_0.2.21              tools_4.4.0              
+ [53] rjson_0.2.21              tools_4.4.1              
  [55] vipor_0.4.7               beeswarm_0.4.0           
  [57] R.oo_1.26.0               glue_1.7.0               
- [59] nlme_3.1-164              grid_4.4.0               
+ [59] nlme_3.1-164              grid_4.4.1               
  [61] cluster_2.1.6             generics_0.1.3           
  [63] gtable_0.3.5              R.methodsS3_1.8.2        
  [65] tidyr_1.3.1               data.table_1.15.4        
@@ -1349,7 +1349,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [71] XVector_0.44.0            ggrepel_0.9.5            
  [73] BiocVersion_3.19.1        pillar_1.9.0             
  [75] limma_3.60.2              BumpyMatrix_1.12.0       
- [77] splines_4.4.0             dplyr_1.1.4              
+ [77] splines_4.4.1             dplyr_1.1.4              
  [79] BiocFileCache_2.12.0      lattice_0.22-6           
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
@@ -1365,7 +1365,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [103] uwot_0.2.2                xtable_1.8-4             
 [105] segmented_2.1-0           munsell_0.5.1            
 [107] Rcpp_1.0.12               dbplyr_2.5.0             
-[109] png_0.1-8                 parallel_4.4.0           
+[109] png_0.1-8                 parallel_4.4.1           
 [111] blob_1.2.4                sparseMatrixStats_1.16.0 
 [113] viridisLite_0.4.2         scales_1.3.0             
 [115] purrr_1.0.2               crayon_1.5.2             
@@ -1396,7 +1396,7 @@ <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
@@ -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" 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>
@@ -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" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -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" 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>
@@ -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" 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>
@@ -1592,7 +1592,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1614,8 +1614,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/cell_type_annotation.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index d4fa5df..c14c147 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory data analysis and quality control</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/eda_qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1429,7 +1429,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1451,8 +1451,8 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/eda_qc.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/hca.html b/instructor/hca.html
index 7e5b51a..9a0af38 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -339,7 +339,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Accessing data from the Human Cell Atlas (HCA)</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/hca.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1008,7 +1008,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1030,8 +1030,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 073932a..735dcc6 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -467,7 +467,7 @@ <h3 id="hca-figure-1">Figure 1</h3>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 91223c0..86bc3e8 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -457,7 +457,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </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">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -483,7 +483,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </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">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</p></li>
@@ -513,7 +513,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </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">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -537,7 +537,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</p></li>
 <li><p>Select the <code>.pkg</code> file for the latest R
@@ -570,7 +570,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
@@ -647,7 +647,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -669,8 +669,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/index.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index b5e5ec2..bc0d83a 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -407,7 +407,7 @@ <h1>Instructor Notes</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 		</footer>
 </div> <!-- / div.container -->
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index cf17199..6102bf0 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -328,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -770,7 +770,7 @@ <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>
@@ -867,7 +867,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -889,8 +889,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 894b36d..ddf8811 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -517,7 +517,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 815c2bc..5f01cf8 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -769,21 +769,20 @@ <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   0   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 203   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0 395   0   1   0   0   1   0   1   0   0   0
-   6    0   0   0   0   0  81 127   0   0   0   1   0   0   0   0
+   1   90   0   0   0   1   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  77   0   1   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 342   0   0   0   0   0   0   0   0   0   0  55
+   5    0   0   0   0  90   0   0  95   0   0   0   8   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
    7    0   0   0   0   0 245   0   0   0   1   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   4  10   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 143   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0   0   0 203   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   6   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  51   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   8    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
+   9    0   0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0   5 142   0   6   0   0
+   11   0   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0 303   0   0   0   0   0   0   0   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</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1058,7 +1057,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1100,7 +1099,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
   [1] RcppAnnoy_0.0.22          later_1.3.2              
-  [3] splines_4.4.0             filelock_1.0.3           
+  [3] splines_4.4.1             filelock_1.0.3           
   [5] tibble_3.2.1              polyclip_1.10-6          
   [7] basilisk.utils_1.16.0     fastDummies_1.7.3        
   [9] lifecycle_1.0.4           edgeR_4.2.0              
@@ -1127,7 +1126,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] viridis_0.6.5             spatstat.explore_3.2-7   
  [53] BiocFileCache_2.12.0      jsonlite_1.8.8           
  [55] progressr_0.14.0          ggridges_0.5.6           
- [57] survival_3.6-4            tools_4.4.0              
+ [57] survival_3.6-4            tools_4.4.1              
  [59] ica_1.0-3                 Rcpp_1.0.12              
  [61] glue_1.7.0                gridExtra_2.3            
  [63] xfun_0.44                 dplyr_1.1.4              
@@ -1152,16 +1151,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
 [105] BiocVersion_3.19.1        KernSmooth_2.23-24       
-[107] parallel_4.4.0            miniUI_0.1.1.1           
+[107] parallel_4.4.1            miniUI_0.1.1.1           
 [109] vipor_0.4.7               AnnotationDbi_1.66.0     
-[111] pillar_1.9.0              grid_4.4.0               
+[111] pillar_1.9.0              grid_4.4.1               
 [113] vctrs_0.6.5               RANN_2.6.1               
 [115] promises_1.3.0            dbplyr_2.5.0             
 [117] beachmat_2.20.0           xtable_1.8-4             
 [119] cluster_2.1.6             beeswarm_0.4.0           
 [121] evaluate_0.23             magick_2.8.3             
 [123] cli_3.6.2                 locfit_1.5-9.9           
-[125] compiler_4.4.0            rlang_1.1.3              
+[125] compiler_4.4.1            rlang_1.1.3              
 [127] crayon_1.5.2              future.apply_1.11.2      
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
@@ -1199,7 +1198,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <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>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1213,7 +1212,7 @@ <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>
@@ -1241,7 +1240,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <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 function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1254,7 +1253,7 @@ <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>
@@ -1284,7 +1283,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1296,7 +1295,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1381,7 +1380,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1403,8 +1402,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index a964d63..781aeb7 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -331,7 +331,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Multi-sample analyses</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/multi-sample.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1123,7 +1123,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1159,7 +1159,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
   [1] DBI_1.2.3                 formatR_1.14             
   [3] gridExtra_2.3             rlang_1.1.3              
-  [5] magrittr_2.0.3            compiler_4.4.0           
+  [5] magrittr_2.0.3            compiler_4.4.1           
   [7] RSQLite_2.3.7             DelayedMatrixStats_1.26.0
   [9] png_0.1-8                 vctrs_0.6.5              
  [11] pkgconfig_2.0.3           crayon_1.5.2             
@@ -1174,9 +1174,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [29] jsonlite_1.8.8            blob_1.2.4               
  [31] highr_0.11                DelayedArray_0.30.1      
  [33] BiocParallel_1.38.0       cluster_2.1.6            
- [35] irlba_2.3.5.1             parallel_4.4.0           
+ [35] irlba_2.3.5.1             parallel_4.4.1           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.47                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.1            
  [41] igraph_2.0.3              Matrix_1.7-0             
  [43] tidyselect_1.2.1          viridis_0.6.5            
  [45] abind_1.4-5               yaml_2.3.8               
@@ -1191,10 +1191,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [63] generics_0.1.3            BiocVersion_3.19.1       
  [65] sparseMatrixStats_1.16.0  munsell_0.5.1            
  [67] scales_1.3.0              glue_1.7.0               
- [69] metapod_1.12.0            tools_4.4.0              
+ [69] metapod_1.12.0            tools_4.4.1              
  [71] AnnotationHub_3.12.0      BiocNeighbors_1.22.0     
  [73] ScaledMatrix_1.12.0       locfit_1.5-9.9           
- [75] cowplot_1.1.3             grid_4.4.0               
+ [75] cowplot_1.1.3             grid_4.4.1               
  [77] AnnotationDbi_1.66.0      colorspace_2.1-0         
  [79] GenomeInfoDbData_1.2.12   beeswarm_0.4.0           
  [81] BiocSingular_1.20.0       vipor_0.4.7              
@@ -1231,7 +1231,7 @@ <h3 class="callout-title">Exercise 1: Replicates<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">
 
 </div>
@@ -1243,7 +1243,7 @@ <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>
@@ -1268,7 +1268,7 @@ <h3 class="callout-title">Exercise 2: <code>muscat</code><a class="anchor" aria-
 <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">
 
 </div>
@@ -1280,7 +1280,7 @@ <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>
@@ -1375,7 +1375,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1397,8 +1397,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/multi-sample.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/multi-sample.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index c9cdcd4..daad7ae 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -330,7 +330,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 13610c9..efe77fc 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -391,7 +391,7 @@ <h1>Reference</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -413,8 +413,8 @@ <h1>Reference</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/reference.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/intro-sce.html b/intro-sce.html
index 14c236b..c0f1cf1 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -328,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -768,7 +768,7 @@ <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>
@@ -865,7 +865,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -887,8 +887,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 2420782..9fccec0 100644
--- a/key-points.html
+++ b/key-points.html
@@ -515,7 +515,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -538,8 +538,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/key-points.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/large_data.html b/large_data.html
index 18bc4bc..cb10014 100644
--- a/large_data.html
+++ b/large_data.html
@@ -333,7 +333,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Working with large data</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/large_data.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -767,21 +767,20 @@ <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   0   0   0   0   1   0   0   0   0   0   0
-   2    0 143   0   1   0   0   0   0   0   0   0   0   0   0   0
-   3    0   0  75   0   2   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 203   0   0   0   0   0   0   0   0 143   0   0
-   5    0   0   0   0 395   0   1   0   0   1   0   1   0   0   0
-   6    0   0   0   0   0  81 127   0   0   0   1   0   0   0   0
+   1   90   0   0   0   1   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  77   0   1   0   0   0   0   0   0   0   0   0   0
+   4    0   0   0 342   0   0   0   0   0   0   0   0   0   0  55
+   5    0   0   0   0  90   0   0  95   0   0   0   8   0   0   0
+   6    0   0   0   0   0  79 131   0   0   0   0   0   0   0   0
    7    0   0   0   0   0 245   0   0   0   1   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   4  10   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 143   0   0   0   0
-   12   0   0   0   0   1   0   0   0   0   0   0 203   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   6   0   0 146   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0   0  20
-   15   0   0   0  51   0   0   0   0   0   0   0   0   0   0   0</code></pre>
+   8    1   0   0   0   1   0   0   0 106   0   0   0   0   0   0
+   9    0   0   0   0   0   0   0   0   0 113   0  10   0   0   0
+   10   0   0   0   0   0   0   0   0   0   5 142   0   6   0   0
+   11   0   0   0   0   0   0   0   0   0   0   0 198   0   0   0
+   12   0   0   0   0 303   0   0   0   0   0   0   0   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</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1056,7 +1055,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1098,7 +1097,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
   [1] RcppAnnoy_0.0.22          later_1.3.2              
-  [3] splines_4.4.0             filelock_1.0.3           
+  [3] splines_4.4.1             filelock_1.0.3           
   [5] tibble_3.2.1              polyclip_1.10-6          
   [7] basilisk.utils_1.16.0     fastDummies_1.7.3        
   [9] lifecycle_1.0.4           edgeR_4.2.0              
@@ -1125,7 +1124,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] viridis_0.6.5             spatstat.explore_3.2-7   
  [53] BiocFileCache_2.12.0      jsonlite_1.8.8           
  [55] progressr_0.14.0          ggridges_0.5.6           
- [57] survival_3.6-4            tools_4.4.0              
+ [57] survival_3.6-4            tools_4.4.1              
  [59] ica_1.0-3                 Rcpp_1.0.12              
  [61] glue_1.7.0                gridExtra_2.3            
  [63] xfun_0.44                 dplyr_1.1.4              
@@ -1150,16 +1149,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
 [105] BiocVersion_3.19.1        KernSmooth_2.23-24       
-[107] parallel_4.4.0            miniUI_0.1.1.1           
+[107] parallel_4.4.1            miniUI_0.1.1.1           
 [109] vipor_0.4.7               AnnotationDbi_1.66.0     
-[111] pillar_1.9.0              grid_4.4.0               
+[111] pillar_1.9.0              grid_4.4.1               
 [113] vctrs_0.6.5               RANN_2.6.1               
 [115] promises_1.3.0            dbplyr_2.5.0             
 [117] beachmat_2.20.0           xtable_1.8-4             
 [119] cluster_2.1.6             beeswarm_0.4.0           
 [121] evaluate_0.23             magick_2.8.3             
 [123] cli_3.6.2                 locfit_1.5-9.9           
-[125] compiler_4.4.0            rlang_1.1.3              
+[125] compiler_4.4.1            rlang_1.1.3              
 [127] crayon_1.5.2              future.apply_1.11.2      
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
@@ -1197,7 +1196,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <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>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1211,7 +1210,7 @@ <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>
@@ -1239,7 +1238,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <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 function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1252,7 +1251,7 @@ <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>
@@ -1282,7 +1281,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1294,7 +1293,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1379,7 +1378,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1401,8 +1400,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/large_data.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index c840ca5..cc68a15 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,17 +1,17 @@
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diff --git a/multi-sample.html b/multi-sample.html
index ec5072b..520e659 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -331,7 +331,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Multi-sample analyses</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/multi-sample.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1121,7 +1121,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>R version 4.4.0 (2024-04-24)
+<pre class="output" tabindex="0"><code>R version 4.4.1 (2024-06-14)
 Platform: x86_64-pc-linux-gnu
 Running under: Ubuntu 22.04.4 LTS
 
@@ -1157,7 +1157,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
   [1] DBI_1.2.3                 formatR_1.14             
   [3] gridExtra_2.3             rlang_1.1.3              
-  [5] magrittr_2.0.3            compiler_4.4.0           
+  [5] magrittr_2.0.3            compiler_4.4.1           
   [7] RSQLite_2.3.7             DelayedMatrixStats_1.26.0
   [9] png_0.1-8                 vctrs_0.6.5              
  [11] pkgconfig_2.0.3           crayon_1.5.2             
@@ -1172,9 +1172,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [29] jsonlite_1.8.8            blob_1.2.4               
  [31] highr_0.11                DelayedArray_0.30.1      
  [33] BiocParallel_1.38.0       cluster_2.1.6            
- [35] irlba_2.3.5.1             parallel_4.4.0           
+ [35] irlba_2.3.5.1             parallel_4.4.1           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.47                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.1            
  [41] igraph_2.0.3              Matrix_1.7-0             
  [43] tidyselect_1.2.1          viridis_0.6.5            
  [45] abind_1.4-5               yaml_2.3.8               
@@ -1189,10 +1189,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [63] generics_0.1.3            BiocVersion_3.19.1       
  [65] sparseMatrixStats_1.16.0  munsell_0.5.1            
  [67] scales_1.3.0              glue_1.7.0               
- [69] metapod_1.12.0            tools_4.4.0              
+ [69] metapod_1.12.0            tools_4.4.1              
  [71] AnnotationHub_3.12.0      BiocNeighbors_1.22.0     
  [73] ScaledMatrix_1.12.0       locfit_1.5-9.9           
- [75] cowplot_1.1.3             grid_4.4.0               
+ [75] cowplot_1.1.3             grid_4.4.1               
  [77] AnnotationDbi_1.66.0      colorspace_2.1-0         
  [79] GenomeInfoDbData_1.2.12   beeswarm_0.4.0           
  [81] BiocSingular_1.20.0       vipor_0.4.7              
@@ -1229,7 +1229,7 @@ <h3 class="callout-title">Exercise 1: Replicates<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">
 
 </div>
@@ -1241,7 +1241,7 @@ <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>
@@ -1266,7 +1266,7 @@ <h3 class="callout-title">Exercise 2: <code>muscat</code><a class="anchor" aria-
 <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">
 
 </div>
@@ -1278,7 +1278,7 @@ <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>
@@ -1373,7 +1373,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1395,8 +1395,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/multi-sample.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index fd1c014..84e3501 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-25T01:01Z
+last_built: 2024-07-02T02:38Z
 
diff --git a/profiles.html b/profiles.html
index cffeeb7..eb8a794 100644
--- a/profiles.html
+++ b/profiles.html
@@ -330,7 +330,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -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": "2024-06-25",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 4c35e8b..7335b6e 100644
--- a/reference.html
+++ b/reference.html
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2024-06-04 |
+        <p>Last updated on 2024-07-02 |
         
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -389,7 +389,7 @@ <h1>Reference</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.5" class="external-link">pegboard (0.7.5)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -411,8 +411,8 @@ <h1>Reference</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/reference.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-06-04",
-  "datePublished": "2024-06-25"
+  "dateModified": "2024-07-02",
+  "datePublished": "2024-07-02"
 }
 
   </script><script>