diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 39bf76c..cf647a3 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -262,7 +262,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -345,7 +345,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/LICENSE.html b/LICENSE.html
index 7dda612..d8fe475 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -262,7 +262,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -396,7 +396,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/aio.html b/aio.html
index 72ebd9e..6b6f0ea 100644
--- a/aio.html
+++ b/aio.html
@@ -310,7 +310,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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">
@@ -758,7 +758,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>
@@ -825,7 +825,7 @@ <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 2024-05-29 |
+<p>Last updated on 2024-06-04 |
         
         <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">
@@ -1005,7 +1005,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1813,7 +1813,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1913,7 +1913,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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">
@@ -2891,7 +2891,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] MouseGastrulationData_1.18.0 SpatialExperiment_1.14.0    
 [15] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [17] Biobase_2.64.0               GenomicRanges_1.56.0        
-[19] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[19] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [21] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [23] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [25] AUCell_1.26.0                BiocStyle_2.32.0            
@@ -2903,24 +2903,24 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   [7] rmarkdown_2.27            zlibbioc_1.50.0          
   [9] vctrs_0.6.5               memoise_2.0.1            
  [11] DelayedMatrixStats_1.26.0 htmltools_0.5.8.1        
- [13] S4Arrays_1.4.0            AnnotationHub_3.12.0     
+ [13] S4Arrays_1.4.1            AnnotationHub_3.12.0     
  [15] curl_5.2.1                BiocNeighbors_1.22.0     
- [17] SparseArray_1.4.3         htmlwidgets_1.6.4        
+ [17] SparseArray_1.4.8         htmlwidgets_1.6.4        
  [19] plotly_4.10.4             cachem_1.1.0             
  [21] igraph_2.0.3              mime_0.12                
  [23] lifecycle_1.0.4           pkgconfig_2.0.3          
  [25] rsvd_1.0.5                Matrix_1.7-0             
  [27] R6_2.5.1                  fastmap_1.2.0            
  [29] GenomeInfoDbData_1.2.12   digest_0.6.35            
- [31] colorspace_2.1-0          dqrng_0.4.0              
+ [31] colorspace_2.1-0          dqrng_0.4.1              
  [33] irlba_2.3.5.1             ExperimentHub_2.12.0     
- [35] RSQLite_2.3.6             beachmat_2.20.0          
+ [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           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
- [47] DBI_1.2.2                 highr_0.10               
+ [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              
@@ -2940,7 +2940,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
  [85] tidyselect_1.2.1          locfit_1.5-9.9           
- [87] Biostrings_2.72.0         knitr_1.46               
+ [87] Biostrings_2.72.1         knitr_1.47               
  [89] gridExtra_2.3             edgeR_4.2.0              
  [91] xfun_0.44                 mixtools_2.0.0           
  [93] statmod_1.5.0             UCSC.utils_1.0.0         
@@ -3149,7 +3149,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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">
@@ -3977,16 +3977,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [7] scuttle_1.14.0               MouseGastrulationData_1.18.0
  [9] SpatialExperiment_1.14.0     SingleCellExperiment_1.26.0 
 [11] SummarizedExperiment_1.34.0  Biobase_2.64.0              
-[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.0         
+[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.1         
 [15] IRanges_2.38.0               S4Vectors_0.42.0            
 [17] BiocGenerics_0.50.0          MatrixGenerics_1.16.0       
 [19] matrixStats_1.3.0            BiocStyle_2.32.0            
 
 loaded via a namespace (and not attached):
-  [1] DBI_1.2.2                 formatR_1.14             
+  [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           
-  [7] RSQLite_2.3.6             DelayedMatrixStats_1.26.0
+  [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             
  [13] fastmap_1.2.0             dbplyr_2.5.0             
@@ -3998,11 +3998,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [25] xfun_0.44                 zlibbioc_1.50.0          
  [27] cachem_1.1.0              beachmat_2.20.0          
  [29] jsonlite_1.8.8            blob_1.2.4               
- [31] highr_0.10                DelayedArray_0.30.1      
+ [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           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.46                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.0            
  [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               
@@ -4011,7 +4011,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] withr_3.0.0               KEGGREST_1.44.0          
  [53] BumpyMatrix_1.12.0        Rtsne_0.17               
  [55] evaluate_0.23             BiocFileCache_2.12.0     
- [57] ExperimentHub_2.12.0      Biostrings_2.72.0        
+ [57] ExperimentHub_2.12.0      Biostrings_2.72.1        
  [59] pillar_1.9.0              BiocManager_1.30.23      
  [61] filelock_1.0.3            renv_1.0.7               
  [63] generics_0.1.3            BiocVersion_3.19.1       
@@ -4026,10 +4026,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] BiocSingular_1.20.0       vipor_0.4.7              
  [83] cli_3.6.2                 rsvd_1.0.5               
  [85] rappdirs_0.3.3            fansi_1.0.6              
- [87] viridisLite_0.4.2         S4Arrays_1.4.0           
+ [87] viridisLite_0.4.2         S4Arrays_1.4.1           
  [89] dplyr_1.1.4               ResidualMatrix_1.14.0    
  [91] gtable_0.3.5              digest_0.6.35            
- [93] dqrng_0.4.0               SparseArray_1.4.3        
+ [93] dqrng_0.4.1               SparseArray_1.4.8        
  [95] ggrepel_0.9.5             farver_2.1.2             
  [97] rjson_0.2.21              memoise_2.0.1            
  [99] htmltools_0.5.8.1         lifecycle_1.0.4          
@@ -4173,7 +4173,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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">
@@ -4611,21 +4611,26 @@ <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   91   0   0   0   0   0   0   0   0   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   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   1
-   5    2   0   0   0 391   0   0   0   0   1   0   0   0   0   0
-   6    0   0   0   0   0 208   1   0   0   0   1   0   0   0   0
-   7    0   0   0   0   0   1 244   0   0   1   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   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
+   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   0   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   3   0   0   0   0   0   0 214   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  55</code></pre>
+   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>
+</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>
+</h3>
+<pre class="error" tabindex="0"><code>Error: rand &gt; 0.85 is not TRUE</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -4634,7 +4639,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 also not difficult to find situations where the approximation
 deteriorates, especially at high dimensions, though this may not have an
 appreciable impact on the biological conclusions.</p>
-<div class="codewrapper sourceCode" id="cb23">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -4669,7 +4674,7 @@ <h3 id="singular-value-decomposition">Singular value decomposition<a class="anch
 change the SVD algorithm used in any of these functions by simply
 specifying an alternative value for the <code>BSPARAM</code>
 argument.</p>
-<div class="codewrapper sourceCode" id="cb25">
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 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4695,7 +4700,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   .. ..$ : chr [1:500] "ENSMUSG00000055609" "ENSMUSG00000052217" "ENSMUSG00000069919" "ENSMUSG00000048583" ...
   .. ..$ : chr [1:20] "PC1" "PC2" "PC3" "PC4" ...</code></pre>
 </div>
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 </h3>
 <pre class="downlit sourceCode r">
@@ -4743,7 +4748,7 @@ <h3 id="seurat">Seurat<a class="anchor" aria-label="anchor" href="#seurat"></a>
 types of single-cell data. Seurat is developed and maintained by the <a href="https://satijalab.org/seurat/authors.html" class="external-link">Satija lab</a> and is
 released under the <a href="https://opensource.org/license/mit/" class="external-link">MIT
 license</a>.</p>
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 </h3>
 <pre class="downlit sourceCode r">
@@ -4765,7 +4770,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 with functionality from OSCA/Bioconductor. We therefore need to first
 install the <a href="https://github.com/satijalab/seurat-data" class="external-link">SeuratData</a> package,
 which is available from GitHub only.</p>
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@@ -4773,7 +4778,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then proceed by loading all required packages and installing the
 PBMC dataset:</p>
-<div class="codewrapper sourceCode" id="cb31">
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 <pre class="downlit sourceCode r">
@@ -4782,7 +4787,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then load the dataset as an <code>SeuratObject</code> and convert
 it to a <code>SingleCellExperiment</code>.</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb33">
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 <pre class="downlit sourceCode r">
@@ -4796,7 +4801,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Seurat also allows conversion from <code>SingleCellExperiment</code>
 objects to Seurat objects; we demonstrate this here on the wild-type
 chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb33">
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 </h3>
 <pre class="downlit sourceCode r">
@@ -4807,7 +4812,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>After some processing of the dataset, the actual conversion is
 carried out with the <code>as.Seurat</code> function.</p>
-<div class="codewrapper sourceCode" id="cb34">
+<div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4840,7 +4845,7 @@ <h3 id="scanpy">Scanpy<a class="anchor" aria-label="anchor" href="#scanpy"></a>
 to enable users and developers to easily move data between these
 frameworks to construct a multi-language analysis pipeline across
 R/Bioconductor and Python.</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4850,7 +4855,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>SingleCellExperiment</code> from an H5AD file. Here, we use an
 example H5AD file contained in the <em><a href="https://bioconductor.org/packages/3.19/zellkonverter" class="external-link">zellkonverter</a></em>
 package.</p>
-<div class="codewrapper sourceCode" id="cb36">
+<div class="codewrapper sourceCode" id="cb37">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4876,7 +4881,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can also write a <code>SingleCellExperiment</code> to an H5AD file
 with the <code>writeH5AD()</code> function. This is demonstrated below
 on the wild-type chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb38">
+<div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4891,7 +4896,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section id="session-info"><h2 class="section-heading">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h2>
 <hr class="half-width">
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4931,11 +4936,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] ggplot2_3.5.1                scuttle_1.14.0              
 [15] TENxBrainData_1.24.0         HDF5Array_1.32.0            
 [17] rhdf5_2.48.0                 DelayedArray_0.30.1         
-[19] SparseArray_1.4.3            S4Arrays_1.4.0              
+[19] SparseArray_1.4.8            S4Arrays_1.4.1              
 [21] abind_1.4-5                  Matrix_1.7-0                
 [23] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [25] Biobase_2.64.0               GenomicRanges_1.56.0        
-[27] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[27] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [29] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [31] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [33] BiocStyle_2.32.0            
@@ -4952,16 +4957,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [17] rmarkdown_2.27            yaml_2.3.8               
  [19] metapod_1.12.0            httpuv_1.6.15            
  [21] sctransform_0.4.1         spam_2.10-0              
- [23] spatstat.sparse_3.0-3     reticulate_1.36.1        
+ [23] spatstat.sparse_3.0-3     reticulate_1.37.0        
  [25] pbapply_1.7-2             cowplot_1.1.3            
- [27] DBI_1.2.2                 RColorBrewer_1.1-3       
+ [27] DBI_1.2.3                 RColorBrewer_1.1-3       
  [29] zlibbioc_1.50.0           Rtsne_0.17               
  [31] purrr_1.0.2               BumpyMatrix_1.12.0       
  [33] rappdirs_0.3.3            GenomeInfoDbData_1.2.12  
  [35] ggrepel_0.9.5             irlba_2.3.5.1            
  [37] spatstat.utils_3.0-4      listenv_0.9.1            
  [39] goftest_1.2-3             RSpectra_0.16-1          
- [41] spatstat.random_3.2-3     dqrng_0.4.0              
+ [41] spatstat.random_3.2-3     dqrng_0.4.1              
  [43] fitdistrplus_1.1-11       parallelly_1.37.1        
  [45] DelayedMatrixStats_1.26.0 leiden_0.4.3.1           
  [47] codetools_0.2-20          tidyselect_1.2.1         
@@ -4980,7 +4985,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [73] R6_2.5.1                  mime_0.12                
  [75] colorspace_2.1-0          scattermore_1.2          
  [77] tensor_1.5                spatstat.data_3.0-4      
- [79] RSQLite_2.3.6             tidyr_1.3.1              
+ [79] RSQLite_2.3.7             tidyr_1.3.1              
  [81] utf8_1.2.4                generics_0.1.3           
  [83] data.table_1.15.4         renv_1.0.7               
  [85] htmlwidgets_1.6.4         httr_1.4.7               
@@ -4989,7 +4994,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [91] lmtest_0.9-40             XVector_0.44.0           
  [93] htmltools_0.5.8.1         dotCall64_1.1-1          
  [95] scales_1.3.0              png_0.1-8                
- [97] knitr_1.46                reshape2_1.4.4           
+ [97] knitr_1.47                reshape2_1.4.4           
  [99] rjson_0.2.21              nlme_3.1-164             
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
@@ -5008,7 +5013,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
 [133] viridisLite_0.4.2         munsell_0.5.1            
-[135] Biostrings_2.72.0         lazyeval_0.2.2           
+[135] Biostrings_2.72.1         lazyeval_0.2.2           
 [137] spatstat.geom_3.2-9       dir.expiry_1.12.0        
 [139] ExperimentHub_2.12.0      RcppHNSW_0.6.0           
 [141] patchwork_1.2.0           sparseMatrixStats_1.16.0 
@@ -5195,7 +5200,7 @@ <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 2024-05-29 |
+<p>Last updated on 2024-06-04 |
         
         <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">
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index ed861c4..6801350 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -280,7 +280,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -1250,7 +1250,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] MouseGastrulationData_1.18.0 SpatialExperiment_1.14.0    
 [15] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [17] Biobase_2.64.0               GenomicRanges_1.56.0        
-[19] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[19] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [21] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [23] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [25] AUCell_1.26.0                BiocStyle_2.32.0            
@@ -1262,24 +1262,24 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   [7] rmarkdown_2.27            zlibbioc_1.50.0          
   [9] vctrs_0.6.5               memoise_2.0.1            
  [11] DelayedMatrixStats_1.26.0 htmltools_0.5.8.1        
- [13] S4Arrays_1.4.0            AnnotationHub_3.12.0     
+ [13] S4Arrays_1.4.1            AnnotationHub_3.12.0     
  [15] curl_5.2.1                BiocNeighbors_1.22.0     
- [17] SparseArray_1.4.3         htmlwidgets_1.6.4        
+ [17] SparseArray_1.4.8         htmlwidgets_1.6.4        
  [19] plotly_4.10.4             cachem_1.1.0             
  [21] igraph_2.0.3              mime_0.12                
  [23] lifecycle_1.0.4           pkgconfig_2.0.3          
  [25] rsvd_1.0.5                Matrix_1.7-0             
  [27] R6_2.5.1                  fastmap_1.2.0            
  [29] GenomeInfoDbData_1.2.12   digest_0.6.35            
- [31] colorspace_2.1-0          dqrng_0.4.0              
+ [31] colorspace_2.1-0          dqrng_0.4.1              
  [33] irlba_2.3.5.1             ExperimentHub_2.12.0     
- [35] RSQLite_2.3.6             beachmat_2.20.0          
+ [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           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
- [47] DBI_1.2.2                 highr_0.10               
+ [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              
@@ -1299,7 +1299,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
  [85] tidyselect_1.2.1          locfit_1.5-9.9           
- [87] Biostrings_2.72.0         knitr_1.46               
+ [87] Biostrings_2.72.1         knitr_1.47               
  [89] gridExtra_2.3             edgeR_4.2.0              
  [91] xfun_0.44                 mixtools_2.0.0           
  [93] statmod_1.5.0             UCSC.utils_1.0.0         
@@ -1559,7 +1559,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/eda_qc.html b/eda_qc.html
index 0edb16f..35fa91c 100644
--- a/eda_qc.html
+++ b/eda_qc.html
@@ -280,7 +280,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -457,7 +457,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1244,7 +1244,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1397,7 +1397,7 @@ <h3 class="callout-title">Further Reading<a class="anchor" aria-label="anchor" h
   "url": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/eda_qc.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/hca.html b/hca.html
index 6645056..ecc609d 100644
--- a/hca.html
+++ b/hca.html
@@ -286,7 +286,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -975,7 +975,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/hca.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index f336bee..665d242 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -262,7 +262,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -347,7 +347,7 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index d24049f..80fd3f9 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -262,7 +262,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -398,7 +398,7 @@ <h1>Licenses</h1>
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/LICENSE.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/aio.html b/instructor/aio.html
index 464f60c..c1d6c00 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -312,7 +312,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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>
@@ -761,7 +761,7 @@ <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>
@@ -828,7 +828,7 @@ <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 2024-05-29 |
+<p>Last updated on 2024-06-04 |
         
         <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>
@@ -1009,7 +1009,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1817,7 +1817,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1917,7 +1917,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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>
@@ -2896,7 +2896,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] MouseGastrulationData_1.18.0 SpatialExperiment_1.14.0    
 [15] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [17] Biobase_2.64.0               GenomicRanges_1.56.0        
-[19] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[19] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [21] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [23] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [25] AUCell_1.26.0                BiocStyle_2.32.0            
@@ -2908,24 +2908,24 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   [7] rmarkdown_2.27            zlibbioc_1.50.0          
   [9] vctrs_0.6.5               memoise_2.0.1            
  [11] DelayedMatrixStats_1.26.0 htmltools_0.5.8.1        
- [13] S4Arrays_1.4.0            AnnotationHub_3.12.0     
+ [13] S4Arrays_1.4.1            AnnotationHub_3.12.0     
  [15] curl_5.2.1                BiocNeighbors_1.22.0     
- [17] SparseArray_1.4.3         htmlwidgets_1.6.4        
+ [17] SparseArray_1.4.8         htmlwidgets_1.6.4        
  [19] plotly_4.10.4             cachem_1.1.0             
  [21] igraph_2.0.3              mime_0.12                
  [23] lifecycle_1.0.4           pkgconfig_2.0.3          
  [25] rsvd_1.0.5                Matrix_1.7-0             
  [27] R6_2.5.1                  fastmap_1.2.0            
  [29] GenomeInfoDbData_1.2.12   digest_0.6.35            
- [31] colorspace_2.1-0          dqrng_0.4.0              
+ [31] colorspace_2.1-0          dqrng_0.4.1              
  [33] irlba_2.3.5.1             ExperimentHub_2.12.0     
- [35] RSQLite_2.3.6             beachmat_2.20.0          
+ [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           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
- [47] DBI_1.2.2                 highr_0.10               
+ [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              
@@ -2945,7 +2945,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
  [85] tidyselect_1.2.1          locfit_1.5-9.9           
- [87] Biostrings_2.72.0         knitr_1.46               
+ [87] Biostrings_2.72.1         knitr_1.47               
  [89] gridExtra_2.3             edgeR_4.2.0              
  [91] xfun_0.44                 mixtools_2.0.0           
  [93] statmod_1.5.0             UCSC.utils_1.0.0         
@@ -3154,7 +3154,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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>
@@ -3983,16 +3983,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [7] scuttle_1.14.0               MouseGastrulationData_1.18.0
  [9] SpatialExperiment_1.14.0     SingleCellExperiment_1.26.0 
 [11] SummarizedExperiment_1.34.0  Biobase_2.64.0              
-[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.0         
+[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.1         
 [15] IRanges_2.38.0               S4Vectors_0.42.0            
 [17] BiocGenerics_0.50.0          MatrixGenerics_1.16.0       
 [19] matrixStats_1.3.0            BiocStyle_2.32.0            
 
 loaded via a namespace (and not attached):
-  [1] DBI_1.2.2                 formatR_1.14             
+  [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           
-  [7] RSQLite_2.3.6             DelayedMatrixStats_1.26.0
+  [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             
  [13] fastmap_1.2.0             dbplyr_2.5.0             
@@ -4004,11 +4004,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [25] xfun_0.44                 zlibbioc_1.50.0          
  [27] cachem_1.1.0              beachmat_2.20.0          
  [29] jsonlite_1.8.8            blob_1.2.4               
- [31] highr_0.10                DelayedArray_0.30.1      
+ [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           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.46                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.0            
  [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               
@@ -4017,7 +4017,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] withr_3.0.0               KEGGREST_1.44.0          
  [53] BumpyMatrix_1.12.0        Rtsne_0.17               
  [55] evaluate_0.23             BiocFileCache_2.12.0     
- [57] ExperimentHub_2.12.0      Biostrings_2.72.0        
+ [57] ExperimentHub_2.12.0      Biostrings_2.72.1        
  [59] pillar_1.9.0              BiocManager_1.30.23      
  [61] filelock_1.0.3            renv_1.0.7               
  [63] generics_0.1.3            BiocVersion_3.19.1       
@@ -4032,10 +4032,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] BiocSingular_1.20.0       vipor_0.4.7              
  [83] cli_3.6.2                 rsvd_1.0.5               
  [85] rappdirs_0.3.3            fansi_1.0.6              
- [87] viridisLite_0.4.2         S4Arrays_1.4.0           
+ [87] viridisLite_0.4.2         S4Arrays_1.4.1           
  [89] dplyr_1.1.4               ResidualMatrix_1.14.0    
  [91] gtable_0.3.5              digest_0.6.35            
- [93] dqrng_0.4.0               SparseArray_1.4.3        
+ [93] dqrng_0.4.1               SparseArray_1.4.8        
  [95] ggrepel_0.9.5             farver_2.1.2             
  [97] rjson_0.2.21              memoise_2.0.1            
  [99] htmltools_0.5.8.1         lifecycle_1.0.4          
@@ -4179,7 +4179,7 @@ <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 2024-05-23 |
+<p>Last updated on 2024-06-04 |
         
         <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>
@@ -4618,21 +4618,26 @@ <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   91   0   0   0   0   0   0   0   0   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   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   1
-   5    2   0   0   0 391   0   0   0   0   1   0   0   0   0   0
-   6    0   0   0   0   0 208   1   0   0   0   1   0   0   0   0
-   7    0   0   0   0   0   1 244   0   0   1   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   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
+   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   0   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   3   0   0   0   0   0   0 214   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  55</code></pre>
+   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>
+</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>
+</h3>
+<pre class="error" tabindex="0"><code>Error: rand &gt; 0.85 is not TRUE</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -4641,7 +4646,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 also not difficult to find situations where the approximation
 deteriorates, especially at high dimensions, though this may not have an
 appreciable impact on the biological conclusions.</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4676,7 +4681,7 @@ <h3 id="singular-value-decomposition">Singular value decomposition<a class="anch
 change the SVD algorithm used in any of these functions by simply
 specifying an alternative value for the <code>BSPARAM</code>
 argument.</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4702,7 +4707,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   .. ..$ : chr [1:500] "ENSMUSG00000055609" "ENSMUSG00000052217" "ENSMUSG00000069919" "ENSMUSG00000048583" ...
   .. ..$ : chr [1:20] "PC1" "PC2" "PC3" "PC4" ...</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4750,7 +4755,7 @@ <h3 id="seurat">Seurat<a class="anchor" aria-label="anchor" href="#seurat"></a>
 types of single-cell data. Seurat is developed and maintained by the <a href="https://satijalab.org/seurat/authors.html" class="external-link">Satija lab</a> and is
 released under the <a href="https://opensource.org/license/mit/" class="external-link">MIT
 license</a>.</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4772,7 +4777,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 with functionality from OSCA/Bioconductor. We therefore need to first
 install the <a href="https://github.com/satijalab/seurat-data" class="external-link">SeuratData</a> package,
 which is available from GitHub only.</p>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4780,7 +4785,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then proceed by loading all required packages and installing the
 PBMC dataset:</p>
-<div class="codewrapper sourceCode" id="cb31">
+<div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4789,7 +4794,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then load the dataset as an <code>SeuratObject</code> and convert
 it to a <code>SingleCellExperiment</code>.</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4803,7 +4808,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Seurat also allows conversion from <code>SingleCellExperiment</code>
 objects to Seurat objects; we demonstrate this here on the wild-type
 chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4814,7 +4819,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>After some processing of the dataset, the actual conversion is
 carried out with the <code>as.Seurat</code> function.</p>
-<div class="codewrapper sourceCode" id="cb34">
+<div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4847,7 +4852,7 @@ <h3 id="scanpy">Scanpy<a class="anchor" aria-label="anchor" href="#scanpy"></a>
 to enable users and developers to easily move data between these
 frameworks to construct a multi-language analysis pipeline across
 R/Bioconductor and Python.</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4857,7 +4862,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>SingleCellExperiment</code> from an H5AD file. Here, we use an
 example H5AD file contained in the <em><a href="https://bioconductor.org/packages/3.19/zellkonverter" class="external-link">zellkonverter</a></em>
 package.</p>
-<div class="codewrapper sourceCode" id="cb36">
+<div class="codewrapper sourceCode" id="cb37">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4883,7 +4888,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can also write a <code>SingleCellExperiment</code> to an H5AD file
 with the <code>writeH5AD()</code> function. This is demonstrated below
 on the wild-type chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb38">
+<div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4898,7 +4903,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section id="session-info"><h2 class="section-heading">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h2>
 <hr class="half-width">
-<div class="codewrapper sourceCode" id="cb39">
+<div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -4938,11 +4943,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] ggplot2_3.5.1                scuttle_1.14.0              
 [15] TENxBrainData_1.24.0         HDF5Array_1.32.0            
 [17] rhdf5_2.48.0                 DelayedArray_0.30.1         
-[19] SparseArray_1.4.3            S4Arrays_1.4.0              
+[19] SparseArray_1.4.8            S4Arrays_1.4.1              
 [21] abind_1.4-5                  Matrix_1.7-0                
 [23] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [25] Biobase_2.64.0               GenomicRanges_1.56.0        
-[27] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[27] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [29] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [31] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [33] BiocStyle_2.32.0            
@@ -4959,16 +4964,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [17] rmarkdown_2.27            yaml_2.3.8               
  [19] metapod_1.12.0            httpuv_1.6.15            
  [21] sctransform_0.4.1         spam_2.10-0              
- [23] spatstat.sparse_3.0-3     reticulate_1.36.1        
+ [23] spatstat.sparse_3.0-3     reticulate_1.37.0        
  [25] pbapply_1.7-2             cowplot_1.1.3            
- [27] DBI_1.2.2                 RColorBrewer_1.1-3       
+ [27] DBI_1.2.3                 RColorBrewer_1.1-3       
  [29] zlibbioc_1.50.0           Rtsne_0.17               
  [31] purrr_1.0.2               BumpyMatrix_1.12.0       
  [33] rappdirs_0.3.3            GenomeInfoDbData_1.2.12  
  [35] ggrepel_0.9.5             irlba_2.3.5.1            
  [37] spatstat.utils_3.0-4      listenv_0.9.1            
  [39] goftest_1.2-3             RSpectra_0.16-1          
- [41] spatstat.random_3.2-3     dqrng_0.4.0              
+ [41] spatstat.random_3.2-3     dqrng_0.4.1              
  [43] fitdistrplus_1.1-11       parallelly_1.37.1        
  [45] DelayedMatrixStats_1.26.0 leiden_0.4.3.1           
  [47] codetools_0.2-20          tidyselect_1.2.1         
@@ -4987,7 +4992,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [73] R6_2.5.1                  mime_0.12                
  [75] colorspace_2.1-0          scattermore_1.2          
  [77] tensor_1.5                spatstat.data_3.0-4      
- [79] RSQLite_2.3.6             tidyr_1.3.1              
+ [79] RSQLite_2.3.7             tidyr_1.3.1              
  [81] utf8_1.2.4                generics_0.1.3           
  [83] data.table_1.15.4         renv_1.0.7               
  [85] htmlwidgets_1.6.4         httr_1.4.7               
@@ -4996,7 +5001,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [91] lmtest_0.9-40             XVector_0.44.0           
  [93] htmltools_0.5.8.1         dotCall64_1.1-1          
  [95] scales_1.3.0              png_0.1-8                
- [97] knitr_1.46                reshape2_1.4.4           
+ [97] knitr_1.47                reshape2_1.4.4           
  [99] rjson_0.2.21              nlme_3.1-164             
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
@@ -5015,7 +5020,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
 [133] viridisLite_0.4.2         munsell_0.5.1            
-[135] Biostrings_2.72.0         lazyeval_0.2.2           
+[135] Biostrings_2.72.1         lazyeval_0.2.2           
 [137] spatstat.geom_3.2-9       dir.expiry_1.12.0        
 [139] ExperimentHub_2.12.0      RcppHNSW_0.6.0           
 [141] patchwork_1.2.0           sparseMatrixStats_1.16.0 
@@ -5202,7 +5207,7 @@ <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 2024-05-29 |
+<p>Last updated on 2024-06-04 |
         
         <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>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index 4db20fd..1bf40c7 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -280,7 +280,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -1252,7 +1252,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] MouseGastrulationData_1.18.0 SpatialExperiment_1.14.0    
 [15] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [17] Biobase_2.64.0               GenomicRanges_1.56.0        
-[19] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[19] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [21] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [23] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [25] AUCell_1.26.0                BiocStyle_2.32.0            
@@ -1264,24 +1264,24 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   [7] rmarkdown_2.27            zlibbioc_1.50.0          
   [9] vctrs_0.6.5               memoise_2.0.1            
  [11] DelayedMatrixStats_1.26.0 htmltools_0.5.8.1        
- [13] S4Arrays_1.4.0            AnnotationHub_3.12.0     
+ [13] S4Arrays_1.4.1            AnnotationHub_3.12.0     
  [15] curl_5.2.1                BiocNeighbors_1.22.0     
- [17] SparseArray_1.4.3         htmlwidgets_1.6.4        
+ [17] SparseArray_1.4.8         htmlwidgets_1.6.4        
  [19] plotly_4.10.4             cachem_1.1.0             
  [21] igraph_2.0.3              mime_0.12                
  [23] lifecycle_1.0.4           pkgconfig_2.0.3          
  [25] rsvd_1.0.5                Matrix_1.7-0             
  [27] R6_2.5.1                  fastmap_1.2.0            
  [29] GenomeInfoDbData_1.2.12   digest_0.6.35            
- [31] colorspace_2.1-0          dqrng_0.4.0              
+ [31] colorspace_2.1-0          dqrng_0.4.1              
  [33] irlba_2.3.5.1             ExperimentHub_2.12.0     
- [35] RSQLite_2.3.6             beachmat_2.20.0          
+ [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           
  [43] bit64_4.0.5               withr_3.0.0              
  [45] BiocParallel_1.38.0       viridis_0.6.5            
- [47] DBI_1.2.2                 highr_0.10               
+ [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              
@@ -1301,7 +1301,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] survival_3.6-4            FNN_1.1.4                
  [83] renv_1.0.7                bit_4.0.5                
  [85] tidyselect_1.2.1          locfit_1.5-9.9           
- [87] Biostrings_2.72.0         knitr_1.46               
+ [87] Biostrings_2.72.1         knitr_1.47               
  [89] gridExtra_2.3             edgeR_4.2.0              
  [91] xfun_0.44                 mixtools_2.0.0           
  [93] statmod_1.5.0             UCSC.utils_1.0.0         
@@ -1561,7 +1561,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/eda_qc.html b/instructor/eda_qc.html
index 0c6cb6f..b462166 100644
--- a/instructor/eda_qc.html
+++ b/instructor/eda_qc.html
@@ -280,7 +280,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -459,7 +459,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Setting the Random Seed</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Whenever your code involves the generation of random numbers, it’s a
 good practice to set the random seed in R with
@@ -1246,7 +1246,7 @@ <h3 class="callout-title">Exercise 2: Dimensionality Reduction<a class="anchor"
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <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>First subset the object to include only highly variable genes
 (<code>sce2 &lt;- sce[hvg.sce.var,]</code>) and then apply the
@@ -1399,7 +1399,7 @@ <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": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/hca.html b/instructor/hca.html
index 2939ac3..4e349fa 100644
--- a/instructor/hca.html
+++ b/instructor/hca.html
@@ -286,7 +286,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -977,7 +977,7 @@ <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": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index c48ea6b..2730c88 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -275,7 +275,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -717,7 +717,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>
@@ -836,7 +836,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/large_data.html b/instructor/large_data.html
index 4b20974..2c01613 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -280,7 +280,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -716,21 +716,26 @@ <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   91   0   0   0   0   0   0   0   0   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   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   1
-   5    2   0   0   0 391   0   0   0   0   1   0   0   0   0   0
-   6    0   0   0   0   0 208   1   0   0   0   1   0   0   0   0
-   7    0   0   0   0   0   1 244   0   0   1   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   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
+   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   0   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   3   0   0   0   0   0   0 214   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  55</code></pre>
+   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>
+</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>
+</h3>
+<pre class="error" tabindex="0"><code>Error: rand &gt; 0.85 is not TRUE</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -739,7 +744,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 also not difficult to find situations where the approximation
 deteriorates, especially at high dimensions, though this may not have an
 appreciable impact on the biological conclusions.</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -773,7 +778,7 @@ <h3 id="singular-value-decomposition">Singular value decomposition<a class="anch
 change the SVD algorithm used in any of these functions by simply
 specifying an alternative value for the <code>BSPARAM</code>
 argument.</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -799,7 +804,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   .. ..$ : chr [1:500] "ENSMUSG00000055609" "ENSMUSG00000052217" "ENSMUSG00000069919" "ENSMUSG00000048583" ...
   .. ..$ : chr [1:20] "PC1" "PC2" "PC3" "PC4" ...</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -845,7 +850,7 @@ <h3 id="seurat">Seurat<a class="anchor" aria-label="anchor" href="#seurat"></a><
 types of single-cell data. Seurat is developed and maintained by the <a href="https://satijalab.org/seurat/authors.html" class="external-link">Satija lab</a> and is
 released under the <a href="https://opensource.org/license/mit/" class="external-link">MIT
 license</a>.</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -867,7 +872,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 with functionality from OSCA/Bioconductor. We therefore need to first
 install the <a href="https://github.com/satijalab/seurat-data" class="external-link">SeuratData</a> package,
 which is available from GitHub only.</p>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -875,7 +880,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then proceed by loading all required packages and installing the
 PBMC dataset:</p>
-<div class="codewrapper sourceCode" id="cb31">
+<div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -884,7 +889,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then load the dataset as an <code>SeuratObject</code> and convert
 it to a <code>SingleCellExperiment</code>.</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -898,7 +903,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Seurat also allows conversion from <code>SingleCellExperiment</code>
 objects to Seurat objects; we demonstrate this here on the wild-type
 chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -909,7 +914,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>After some processing of the dataset, the actual conversion is
 carried out with the <code>as.Seurat</code> function.</p>
-<div class="codewrapper sourceCode" id="cb34">
+<div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -941,7 +946,7 @@ <h3 id="scanpy">Scanpy<a class="anchor" aria-label="anchor" href="#scanpy"></a><
 to enable users and developers to easily move data between these
 frameworks to construct a multi-language analysis pipeline across
 R/Bioconductor and Python.</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -951,7 +956,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>SingleCellExperiment</code> from an H5AD file. Here, we use an
 example H5AD file contained in the <em><a href="https://bioconductor.org/packages/3.19/zellkonverter" class="external-link">zellkonverter</a></em>
 package.</p>
-<div class="codewrapper sourceCode" id="cb36">
+<div class="codewrapper sourceCode" id="cb37">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -977,7 +982,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can also write a <code>SingleCellExperiment</code> to an H5AD file
 with the <code>writeH5AD()</code> function. This is demonstrated below
 on the wild-type chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb38">
+<div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -991,7 +996,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </section><section id="session-info"><h2 class="section-heading">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h2>
-<hr class="half-width"><div class="codewrapper sourceCode" id="cb39">
+<hr class="half-width"><div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -1031,11 +1036,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] ggplot2_3.5.1                scuttle_1.14.0              
 [15] TENxBrainData_1.24.0         HDF5Array_1.32.0            
 [17] rhdf5_2.48.0                 DelayedArray_0.30.1         
-[19] SparseArray_1.4.3            S4Arrays_1.4.0              
+[19] SparseArray_1.4.8            S4Arrays_1.4.1              
 [21] abind_1.4-5                  Matrix_1.7-0                
 [23] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [25] Biobase_2.64.0               GenomicRanges_1.56.0        
-[27] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[27] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [29] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [31] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [33] BiocStyle_2.32.0            
@@ -1052,16 +1057,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [17] rmarkdown_2.27            yaml_2.3.8               
  [19] metapod_1.12.0            httpuv_1.6.15            
  [21] sctransform_0.4.1         spam_2.10-0              
- [23] spatstat.sparse_3.0-3     reticulate_1.36.1        
+ [23] spatstat.sparse_3.0-3     reticulate_1.37.0        
  [25] pbapply_1.7-2             cowplot_1.1.3            
- [27] DBI_1.2.2                 RColorBrewer_1.1-3       
+ [27] DBI_1.2.3                 RColorBrewer_1.1-3       
  [29] zlibbioc_1.50.0           Rtsne_0.17               
  [31] purrr_1.0.2               BumpyMatrix_1.12.0       
  [33] rappdirs_0.3.3            GenomeInfoDbData_1.2.12  
  [35] ggrepel_0.9.5             irlba_2.3.5.1            
  [37] spatstat.utils_3.0-4      listenv_0.9.1            
  [39] goftest_1.2-3             RSpectra_0.16-1          
- [41] spatstat.random_3.2-3     dqrng_0.4.0              
+ [41] spatstat.random_3.2-3     dqrng_0.4.1              
  [43] fitdistrplus_1.1-11       parallelly_1.37.1        
  [45] DelayedMatrixStats_1.26.0 leiden_0.4.3.1           
  [47] codetools_0.2-20          tidyselect_1.2.1         
@@ -1080,7 +1085,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [73] R6_2.5.1                  mime_0.12                
  [75] colorspace_2.1-0          scattermore_1.2          
  [77] tensor_1.5                spatstat.data_3.0-4      
- [79] RSQLite_2.3.6             tidyr_1.3.1              
+ [79] RSQLite_2.3.7             tidyr_1.3.1              
  [81] utf8_1.2.4                generics_0.1.3           
  [83] data.table_1.15.4         renv_1.0.7               
  [85] htmlwidgets_1.6.4         httr_1.4.7               
@@ -1089,7 +1094,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [91] lmtest_0.9-40             XVector_0.44.0           
  [93] htmltools_0.5.8.1         dotCall64_1.1-1          
  [95] scales_1.3.0              png_0.1-8                
- [97] knitr_1.46                reshape2_1.4.4           
+ [97] knitr_1.47                reshape2_1.4.4           
  [99] rjson_0.2.21              nlme_3.1-164             
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
@@ -1108,7 +1113,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
 [133] viridisLite_0.4.2         munsell_0.5.1            
-[135] Biostrings_2.72.0         lazyeval_0.2.2           
+[135] Biostrings_2.72.1         lazyeval_0.2.2           
 [137] spatstat.geom_3.2-9       dir.expiry_1.12.0        
 [139] ExperimentHub_2.12.0      RcppHNSW_0.6.0           
 [141] patchwork_1.2.0           sparseMatrixStats_1.16.0 
@@ -1345,7 +1350,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/multi-sample.html b/instructor/multi-sample.html
index 67a09b3..11607ae 100644
--- a/instructor/multi-sample.html
+++ b/instructor/multi-sample.html
@@ -278,7 +278,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -1098,16 +1098,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [7] scuttle_1.14.0               MouseGastrulationData_1.18.0
  [9] SpatialExperiment_1.14.0     SingleCellExperiment_1.26.0 
 [11] SummarizedExperiment_1.34.0  Biobase_2.64.0              
-[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.0         
+[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.1         
 [15] IRanges_2.38.0               S4Vectors_0.42.0            
 [17] BiocGenerics_0.50.0          MatrixGenerics_1.16.0       
 [19] matrixStats_1.3.0            BiocStyle_2.32.0            
 
 loaded via a namespace (and not attached):
-  [1] DBI_1.2.2                 formatR_1.14             
+  [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           
-  [7] RSQLite_2.3.6             DelayedMatrixStats_1.26.0
+  [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             
  [13] fastmap_1.2.0             dbplyr_2.5.0             
@@ -1119,11 +1119,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [25] xfun_0.44                 zlibbioc_1.50.0          
  [27] cachem_1.1.0              beachmat_2.20.0          
  [29] jsonlite_1.8.8            blob_1.2.4               
- [31] highr_0.10                DelayedArray_0.30.1      
+ [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           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.46                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.0            
  [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               
@@ -1132,7 +1132,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] withr_3.0.0               KEGGREST_1.44.0          
  [53] BumpyMatrix_1.12.0        Rtsne_0.17               
  [55] evaluate_0.23             BiocFileCache_2.12.0     
- [57] ExperimentHub_2.12.0      Biostrings_2.72.0        
+ [57] ExperimentHub_2.12.0      Biostrings_2.72.1        
  [59] pillar_1.9.0              BiocManager_1.30.23      
  [61] filelock_1.0.3            renv_1.0.7               
  [63] generics_0.1.3            BiocVersion_3.19.1       
@@ -1147,10 +1147,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] BiocSingular_1.20.0       vipor_0.4.7              
  [83] cli_3.6.2                 rsvd_1.0.5               
  [85] rappdirs_0.3.3            fansi_1.0.6              
- [87] viridisLite_0.4.2         S4Arrays_1.4.0           
+ [87] viridisLite_0.4.2         S4Arrays_1.4.1           
  [89] dplyr_1.1.4               ResidualMatrix_1.14.0    
  [91] gtable_0.3.5              digest_0.6.35            
- [93] dqrng_0.4.0               SparseArray_1.4.3        
+ [93] dqrng_0.4.1               SparseArray_1.4.8        
  [95] ggrepel_0.9.5             farver_2.1.2             
  [97] rjson_0.2.21              memoise_2.0.1            
  [99] htmltools_0.5.8.1         lifecycle_1.0.4          
@@ -1344,7 +1344,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/instructor/reference.html b/instructor/reference.html
index c6fab33..746d0b9 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -262,7 +262,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -360,7 +360,7 @@ <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": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/intro-sce.html b/intro-sce.html
index 29fe37e..d9790e0 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -275,7 +275,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -715,7 +715,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" 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>
@@ -834,7 +834,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/large_data.html b/large_data.html
index 1ea66b0..703de6d 100644
--- a/large_data.html
+++ b/large_data.html
@@ -280,7 +280,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -714,21 +714,26 @@ <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   91   0   0   0   0   0   0   0   0   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   0   0   0   0   0   0   0   0   0   0   0
-   4    0   0   0 341   0   0   0   0   0   0   0   0   0   0   1
-   5    2   0   0   0 391   0   0   0   0   1   0   0   0   0   0
-   6    0   0   0   0   0 208   1   0   0   0   1   0   0   0   0
-   7    0   0   0   0   0   1 244   0   0   1   0   0   0   0   0
+   1   90   0   0   0   0   0   0   0   1   0   0   0   0   0   0
+   2    0 143   0   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
+   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   0   0   0   0   0
-   11   0   0   0   0   0   0   0   0   0   0 153   0   0   0   0
-   12   0   0   0   0   3   0   0   0   0   0   0 214   0   0   0
-   13   0   0   0   0   0   0   0   0   0   0   0   0 146   0   0
-   14   0   0   0   0   0   0   0   0   0   0   0   0   0  20   0
-   15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  55</code></pre>
+   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>
+</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>
+</h3>
+<pre class="error" tabindex="0"><code>Error: rand &gt; 0.85 is not TRUE</code></pre>
 </div>
 <p>Note that Annoy writes the NN index to disk prior to performing the
 search. Thus, it may not actually be faster than the default exact
@@ -737,7 +742,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 also not difficult to find situations where the approximation
 deteriorates, especially at high dimensions, though this may not have an
 appreciable impact on the biological conclusions.</p>
-<div class="codewrapper sourceCode" id="cb23">
+<div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -771,7 +776,7 @@ <h3 id="singular-value-decomposition">Singular value decomposition<a class="anch
 change the SVD algorithm used in any of these functions by simply
 specifying an alternative value for the <code>BSPARAM</code>
 argument.</p>
-<div class="codewrapper sourceCode" id="cb25">
+<div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -797,7 +802,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   .. ..$ : chr [1:500] "ENSMUSG00000055609" "ENSMUSG00000052217" "ENSMUSG00000069919" "ENSMUSG00000048583" ...
   .. ..$ : chr [1:20] "PC1" "PC2" "PC3" "PC4" ...</code></pre>
 </div>
-<div class="codewrapper sourceCode" id="cb27">
+<div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -843,7 +848,7 @@ <h3 id="seurat">Seurat<a class="anchor" aria-label="anchor" href="#seurat"></a><
 types of single-cell data. Seurat is developed and maintained by the <a href="https://satijalab.org/seurat/authors.html" class="external-link">Satija lab</a> and is
 released under the <a href="https://opensource.org/license/mit/" class="external-link">MIT
 license</a>.</p>
-<div class="codewrapper sourceCode" id="cb29">
+<div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -865,7 +870,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 with functionality from OSCA/Bioconductor. We therefore need to first
 install the <a href="https://github.com/satijalab/seurat-data" class="external-link">SeuratData</a> package,
 which is available from GitHub only.</p>
-<div class="codewrapper sourceCode" id="cb30">
+<div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -873,7 +878,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then proceed by loading all required packages and installing the
 PBMC dataset:</p>
-<div class="codewrapper sourceCode" id="cb31">
+<div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -882,7 +887,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>We then load the dataset as an <code>SeuratObject</code> and convert
 it to a <code>SingleCellExperiment</code>.</p>
-<div class="codewrapper sourceCode" id="cb32">
+<div class="codewrapper sourceCode" id="cb33">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -896,7 +901,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Seurat also allows conversion from <code>SingleCellExperiment</code>
 objects to Seurat objects; we demonstrate this here on the wild-type
 chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb33">
+<div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -907,7 +912,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 <p>After some processing of the dataset, the actual conversion is
 carried out with the <code>as.Seurat</code> function.</p>
-<div class="codewrapper sourceCode" id="cb34">
+<div class="codewrapper sourceCode" id="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -939,7 +944,7 @@ <h3 id="scanpy">Scanpy<a class="anchor" aria-label="anchor" href="#scanpy"></a><
 to enable users and developers to easily move data between these
 frameworks to construct a multi-language analysis pipeline across
 R/Bioconductor and Python.</p>
-<div class="codewrapper sourceCode" id="cb35">
+<div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -949,7 +954,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code>SingleCellExperiment</code> from an H5AD file. Here, we use an
 example H5AD file contained in the <em><a href="https://bioconductor.org/packages/3.19/zellkonverter" class="external-link">zellkonverter</a></em>
 package.</p>
-<div class="codewrapper sourceCode" id="cb36">
+<div class="codewrapper sourceCode" id="cb37">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -975,7 +980,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>We can also write a <code>SingleCellExperiment</code> to an H5AD file
 with the <code>writeH5AD()</code> function. This is demonstrated below
 on the wild-type chimera mouse gastrulation dataset.</p>
-<div class="codewrapper sourceCode" id="cb38">
+<div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -989,7 +994,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </section><section id="session-info"><h2 class="section-heading">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a>
 </h2>
-<hr class="half-width"><div class="codewrapper sourceCode" id="cb39">
+<hr class="half-width"><div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="downlit sourceCode r">
@@ -1029,11 +1034,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [13] ggplot2_3.5.1                scuttle_1.14.0              
 [15] TENxBrainData_1.24.0         HDF5Array_1.32.0            
 [17] rhdf5_2.48.0                 DelayedArray_0.30.1         
-[19] SparseArray_1.4.3            S4Arrays_1.4.0              
+[19] SparseArray_1.4.8            S4Arrays_1.4.1              
 [21] abind_1.4-5                  Matrix_1.7-0                
 [23] SingleCellExperiment_1.26.0  SummarizedExperiment_1.34.0 
 [25] Biobase_2.64.0               GenomicRanges_1.56.0        
-[27] GenomeInfoDb_1.40.0          IRanges_2.38.0              
+[27] GenomeInfoDb_1.40.1          IRanges_2.38.0              
 [29] S4Vectors_0.42.0             BiocGenerics_0.50.0         
 [31] MatrixGenerics_1.16.0        matrixStats_1.3.0           
 [33] BiocStyle_2.32.0            
@@ -1050,16 +1055,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [17] rmarkdown_2.27            yaml_2.3.8               
  [19] metapod_1.12.0            httpuv_1.6.15            
  [21] sctransform_0.4.1         spam_2.10-0              
- [23] spatstat.sparse_3.0-3     reticulate_1.36.1        
+ [23] spatstat.sparse_3.0-3     reticulate_1.37.0        
  [25] pbapply_1.7-2             cowplot_1.1.3            
- [27] DBI_1.2.2                 RColorBrewer_1.1-3       
+ [27] DBI_1.2.3                 RColorBrewer_1.1-3       
  [29] zlibbioc_1.50.0           Rtsne_0.17               
  [31] purrr_1.0.2               BumpyMatrix_1.12.0       
  [33] rappdirs_0.3.3            GenomeInfoDbData_1.2.12  
  [35] ggrepel_0.9.5             irlba_2.3.5.1            
  [37] spatstat.utils_3.0-4      listenv_0.9.1            
  [39] goftest_1.2-3             RSpectra_0.16-1          
- [41] spatstat.random_3.2-3     dqrng_0.4.0              
+ [41] spatstat.random_3.2-3     dqrng_0.4.1              
  [43] fitdistrplus_1.1-11       parallelly_1.37.1        
  [45] DelayedMatrixStats_1.26.0 leiden_0.4.3.1           
  [47] codetools_0.2-20          tidyselect_1.2.1         
@@ -1078,7 +1083,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [73] R6_2.5.1                  mime_0.12                
  [75] colorspace_2.1-0          scattermore_1.2          
  [77] tensor_1.5                spatstat.data_3.0-4      
- [79] RSQLite_2.3.6             tidyr_1.3.1              
+ [79] RSQLite_2.3.7             tidyr_1.3.1              
  [81] utf8_1.2.4                generics_0.1.3           
  [83] data.table_1.15.4         renv_1.0.7               
  [85] htmlwidgets_1.6.4         httr_1.4.7               
@@ -1087,7 +1092,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [91] lmtest_0.9-40             XVector_0.44.0           
  [93] htmltools_0.5.8.1         dotCall64_1.1-1          
  [95] scales_1.3.0              png_0.1-8                
- [97] knitr_1.46                reshape2_1.4.4           
+ [97] knitr_1.47                reshape2_1.4.4           
  [99] rjson_0.2.21              nlme_3.1-164             
 [101] curl_5.2.1                cachem_1.1.0             
 [103] zoo_1.8-12                stringr_1.5.1            
@@ -1106,7 +1111,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [129] plyr_1.8.9                ggbeeswarm_0.7.2         
 [131] stringi_1.8.4             deldir_2.0-4             
 [133] viridisLite_0.4.2         munsell_0.5.1            
-[135] Biostrings_2.72.0         lazyeval_0.2.2           
+[135] Biostrings_2.72.1         lazyeval_0.2.2           
 [137] spatstat.geom_3.2-9       dir.expiry_1.12.0        
 [139] ExperimentHub_2.12.0      RcppHNSW_0.6.0           
 [141] patchwork_1.2.0           sparseMatrixStats_1.16.0 
@@ -1343,7 +1348,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/md5sum.txt b/md5sum.txt
index 288fc28..c840ca5 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,17 +1,17 @@
 "file" "checksum" "built" "date"
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-"episodes/intro-sce.Rmd" "fffab405c45c9b0e52a5c34070958b65" "site/built/intro-sce.md" "2024-05-23"
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-"episodes/cell_type_annotation.Rmd" "0aee6fee81ace65c93a9e39b0916a2cb" "site/built/cell_type_annotation.md" "2024-05-23"
-"episodes/multi-sample.Rmd" "75798a2bb3500220ff7b3c1d88cadf41" "site/built/multi-sample.md" "2024-05-23"
-"episodes/large_data.Rmd" "6b413ccf15bea3e70c6dd75432d3914d" "site/built/large_data.md" "2024-05-23"
-"episodes/hca.Rmd" "09e4390a2d357fdb950d663f3d3fcd7a" "site/built/hca.md" "2024-05-29"
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-"renv/profiles/lesson-requirements/renv.lock" "fc493dfccc9d998ded2f8d4ce300273e" "site/built/renv.lock" "2024-05-23"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-06-04"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-06-04"
+"config.yaml" "b0d664d3d6abdd0e98b16282e1c03107" "site/built/config.yaml" "2024-06-04"
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+"episodes/intro-sce.Rmd" "fffab405c45c9b0e52a5c34070958b65" "site/built/intro-sce.md" "2024-06-04"
+"episodes/eda_qc.Rmd" "fac7397fb4caf04a9dc411b5e316ed60" "site/built/eda_qc.md" "2024-06-04"
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+"episodes/multi-sample.Rmd" "75798a2bb3500220ff7b3c1d88cadf41" "site/built/multi-sample.md" "2024-06-04"
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diff --git a/multi-sample.html b/multi-sample.html
index 739fb66..a509284 100644
--- a/multi-sample.html
+++ b/multi-sample.html
@@ -278,7 +278,7 @@ <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 2024-05-23 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -1096,16 +1096,16 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [7] scuttle_1.14.0               MouseGastrulationData_1.18.0
  [9] SpatialExperiment_1.14.0     SingleCellExperiment_1.26.0 
 [11] SummarizedExperiment_1.34.0  Biobase_2.64.0              
-[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.0         
+[13] GenomicRanges_1.56.0         GenomeInfoDb_1.40.1         
 [15] IRanges_2.38.0               S4Vectors_0.42.0            
 [17] BiocGenerics_0.50.0          MatrixGenerics_1.16.0       
 [19] matrixStats_1.3.0            BiocStyle_2.32.0            
 
 loaded via a namespace (and not attached):
-  [1] DBI_1.2.2                 formatR_1.14             
+  [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           
-  [7] RSQLite_2.3.6             DelayedMatrixStats_1.26.0
+  [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             
  [13] fastmap_1.2.0             dbplyr_2.5.0             
@@ -1117,11 +1117,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [25] xfun_0.44                 zlibbioc_1.50.0          
  [27] cachem_1.1.0              beachmat_2.20.0          
  [29] jsonlite_1.8.8            blob_1.2.4               
- [31] highr_0.10                DelayedArray_0.30.1      
+ [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           
  [37] R6_2.5.1                  Rcpp_1.0.12              
- [39] knitr_1.46                splines_4.4.0            
+ [39] knitr_1.47                splines_4.4.0            
  [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               
@@ -1130,7 +1130,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [51] withr_3.0.0               KEGGREST_1.44.0          
  [53] BumpyMatrix_1.12.0        Rtsne_0.17               
  [55] evaluate_0.23             BiocFileCache_2.12.0     
- [57] ExperimentHub_2.12.0      Biostrings_2.72.0        
+ [57] ExperimentHub_2.12.0      Biostrings_2.72.1        
  [59] pillar_1.9.0              BiocManager_1.30.23      
  [61] filelock_1.0.3            renv_1.0.7               
  [63] generics_0.1.3            BiocVersion_3.19.1       
@@ -1145,10 +1145,10 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [81] BiocSingular_1.20.0       vipor_0.4.7              
  [83] cli_3.6.2                 rsvd_1.0.5               
  [85] rappdirs_0.3.3            fansi_1.0.6              
- [87] viridisLite_0.4.2         S4Arrays_1.4.0           
+ [87] viridisLite_0.4.2         S4Arrays_1.4.1           
  [89] dplyr_1.1.4               ResidualMatrix_1.14.0    
  [91] gtable_0.3.5              digest_0.6.35            
- [93] dqrng_0.4.0               SparseArray_1.4.3        
+ [93] dqrng_0.4.1               SparseArray_1.4.8        
  [95] ggrepel_0.9.5             farver_2.1.2             
  [97] rjson_0.2.21              memoise_2.0.1            
  [99] htmltools_0.5.8.1         lifecycle_1.0.4          
@@ -1342,7 +1342,7 @@ <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": "2024-05-23",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }
 
diff --git a/pkgdown.yml b/pkgdown.yml
index def32d0..cdf2e49 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-04T00:36Z
+last_built: 2024-06-04T10:50Z
 
diff --git a/reference.html b/reference.html
index 88e4f15..b8bd015 100644
--- a/reference.html
+++ b/reference.html
@@ -262,7 +262,7 @@ <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 2024-05-29 |
+        <p>Last updated on 2024-06-04 |
         
         <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>
         
@@ -358,7 +358,7 @@ <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": "2024-05-29",
+  "dateModified": "2024-06-04",
   "datePublished": "2024-06-04"
 }