diff --git a/01-intro-to-rnaseq.html b/01-intro-to-rnaseq.html
index cd9ebbc1..acd76be6 100644
--- a/01-intro-to-rnaseq.html
+++ b/01-intro-to-rnaseq.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 RNA-seq</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/01-intro-to-rnaseq.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -661,7 +661,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/01-intro-to-rnaseq.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/01-intro-to-rnaseq.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/02-setup.html b/02-setup.html
index 4a3999e5..0eedff5b 100644
--- a/02-setup.html
+++ b/02-setup.html
@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>RStudio Project and Experimental Data</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/02-setup.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -653,7 +653,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/02-setup.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/02-setup.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/03-import-annotate.html b/03-import-annotate.html
index b3d0ba48..4d105f01 100644
--- a/03-import-annotate.html
+++ b/03-import-annotate.html
@@ -288,7 +288,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Importing and annotating quantified data into R</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/03-import-annotate.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -524,7 +524,7 @@ <h3 class="callout-title">Challenge: Discuss the following points with
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>In <code>counts</code>, the rows are genes just like the rows in
 <code>rowranges</code>. The columns in <code>counts</code> are the
@@ -644,7 +644,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1021,7 +1021,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1148,7 +1148,7 @@ <h3 class="callout-title">Challenge: How to subset to mRNA genes<a class="anchor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb55">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1332,23 +1332,23 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [1] hgu95av2.db_3.13.0          org.Hs.eg.db_3.17.0        
  [3] org.Mm.eg.db_3.17.0         AnnotationDbi_1.62.2       
  [5] SummarizedExperiment_1.30.2 Biobase_2.60.0             
- [7] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+ [7] MatrixGenerics_1.12.3       matrixStats_1.2.0          
  [9] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [11] IRanges_2.34.1              S4Vectors_0.38.2           
 [13] BiocGenerics_0.46.0         knitr_1.45                 
 
 loaded via a namespace (and not attached):
- [1] Matrix_1.6-1.1          bit_4.0.5               highr_0.10             
+ [1] Matrix_1.6-4            bit_4.0.5               highr_0.10             
  [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.3             
  [7] crayon_1.5.2            blob_1.2.4              Biostrings_2.68.1      
 [10] bitops_1.0-7            png_0.1-8               fastmap_1.1.1          
-[13] yaml_2.3.7              lattice_0.22-5          R6_2.5.1               
+[13] yaml_2.3.8              lattice_0.22-5          R6_2.5.1               
 [16] XVector_0.40.0          S4Arrays_1.0.6          DelayedArray_0.26.7    
-[19] GenomeInfoDbData_1.2.10 DBI_1.1.3               rlang_1.1.2            
+[19] GenomeInfoDbData_1.2.10 DBI_1.2.0               rlang_1.1.2            
 [22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.41              
-[25] bit64_4.0.5             RSQLite_2.3.3           memoise_2.0.1          
-[28] cli_3.6.1               zlibbioc_1.46.0         grid_4.3.2             
-[31] vctrs_0.6.4             evaluate_0.23           abind_1.4-5            
+[25] bit64_4.0.5             RSQLite_2.3.4           memoise_2.0.1          
+[28] cli_3.6.2               zlibbioc_1.46.0         grid_4.3.2             
+[31] vctrs_0.6.5             evaluate_0.23           abind_1.4-5            
 [34] RCurl_1.98-1.13         httr_1.4.7              pkgconfig_2.0.3        
 [37] tools_4.3.2            </code></pre>
 </div>
@@ -1424,7 +1424,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/03-import-annotate.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/04-exploratory-qc.html b/04-exploratory-qc.html
index bb85d506..e35a6678 100644
--- a/04-exploratory-qc.html
+++ b/04-exploratory-qc.html
@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory analysis and quality control</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/04-exploratory-qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -834,7 +834,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [5] ComplexHeatmap_2.16.0       ggplot2_3.4.4              
  [7] vsn_3.68.0                  DESeq2_1.40.2              
  [9] SummarizedExperiment_1.30.2 Biobase_2.60.0             
-[11] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+[11] MatrixGenerics_1.12.3       matrixStats_1.2.0          
 [13] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [15] IRanges_2.34.1              S4Vectors_0.38.2           
 [17] BiocGenerics_0.46.0        
@@ -842,34 +842,34 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
  [1] bitops_1.0-7            rlang_1.1.2             magrittr_2.0.3         
  [4] shinydashboard_0.7.2    clue_0.3-65             GetoptLong_1.0.5       
- [7] compiler_4.3.2          mgcv_1.9-0              png_0.1-8              
-[10] vctrs_0.6.4             pkgconfig_2.0.3         shape_1.4.6            
+ [7] compiler_4.3.2          mgcv_1.9-1              png_0.1-8              
+[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6            
 [13] crayon_1.5.2            fastmap_1.1.1           XVector_0.40.0         
 [16] ellipsis_0.3.2          labeling_0.4.3          utf8_1.2.4             
 [19] promises_1.2.1          preprocessCore_1.62.1   shinyAce_0.4.2         
 [22] xfun_0.41               cachem_1.0.8            zlibbioc_1.46.0        
-[25] jsonlite_1.8.7          highr_0.10              later_1.3.1            
+[25] jsonlite_1.8.8          highr_0.10              later_1.3.2            
 [28] DelayedArray_0.26.7     BiocParallel_1.34.2     parallel_4.3.2         
-[31] cluster_2.1.4           R6_2.5.1                bslib_0.5.1            
+[31] cluster_2.1.6           R6_2.5.1                bslib_0.6.1            
 [34] limma_3.56.2            jquerylib_0.1.4         Rcpp_1.0.11            
-[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.12          
-[40] Matrix_1.6-1.1          splines_4.3.2           igraph_1.5.1           
-[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.7             
+[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.13          
+[40] Matrix_1.6-4            splines_4.3.2           igraph_1.6.0           
+[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.8             
 [46] doParallel_1.0.17       codetools_0.2-19        affy_1.78.2            
 [49] miniUI_0.1.1.1          lattice_0.22-5          tibble_3.2.1           
-[52] shiny_1.7.5.1           withr_2.5.2             evaluate_0.23          
+[52] shiny_1.8.0             withr_2.5.2             evaluate_0.23          
 [55] circlize_0.4.15         pillar_1.9.0            affyio_1.70.0          
-[58] BiocManager_1.30.22     renv_1.0.3              DT_0.30                
+[58] BiocManager_1.30.22     renv_1.0.3              DT_0.31                
 [61] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3         
-[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.2.1           
+[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.3.0           
 [67] xtable_1.8-4            glue_1.6.2              tools_4.3.2            
 [70] colourpicker_1.3.0      locfit_1.5-9.8          colorspace_2.1-0       
-[73] nlme_3.1-163            GenomeInfoDbData_1.2.10 vipor_0.4.5            
-[76] cli_3.6.1               fansi_1.0.5             viridisLite_0.4.2      
-[79] S4Arrays_1.0.6          dplyr_1.1.3             gtable_0.3.4           
-[82] rintrojs_0.3.3          sass_0.4.7              digest_0.6.33          
+[73] nlme_3.1-164            GenomeInfoDbData_1.2.10 vipor_0.4.7            
+[76] cli_3.6.2               fansi_1.0.6             viridisLite_0.4.2      
+[79] S4Arrays_1.0.6          dplyr_1.1.4             gtable_0.3.4           
+[82] rintrojs_0.3.3          sass_0.4.8              digest_0.6.33          
 [85] ggrepel_0.9.4           farver_2.1.1            rjson_0.2.21           
-[88] htmlwidgets_1.6.2       htmltools_0.5.7         lifecycle_1.0.3        
+[88] htmlwidgets_1.6.4       htmltools_0.5.7         lifecycle_1.0.4        
 [91] shinyWidgets_0.8.0      GlobalOptions_0.1.2     mime_0.12              </code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
@@ -944,7 +944,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/04-exploratory-qc.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/05-differential-expression.html b/05-differential-expression.html
index 72f7e7d5..3a7423b9 100644
--- a/05-differential-expression.html
+++ b/05-differential-expression.html
@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Differential expression analysis</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/05-differential-expression.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1025,7 +1025,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/05-differential-expression.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/06-extra-design.html b/06-extra-design.html
index f4a88a85..c84ce0a9 100644
--- a/06-extra-design.html
+++ b/06-extra-design.html
@@ -291,7 +291,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Extra exploration of design matrices</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/06-extra-design.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -657,7 +657,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -744,7 +744,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1999,7 +1999,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/06-extra-design.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/07-gene-set-analysis.html b/07-gene-set-analysis.html
index 676f350e..7c071ccd 100644
--- a/07-gene-set-analysis.html
+++ b/07-gene-set-analysis.html
@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Gene set enrichment analysis</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/07-gene-set-analysis.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -842,9 +842,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>Unit: microseconds
-   expr     min      lq      mean   median       uq     max neval
- fisher 238.465 243.715 252.68149 246.8705 252.3760 488.411   100
-  hyper   1.352   1.543   2.23699   2.5545   2.8355   5.901   100</code></pre>
+   expr     min       lq      mean   median       uq     max neval
+ fisher 238.455 241.8405 250.98679 244.1705 251.2475 552.429   100
+  hyper   1.332   1.5180   2.38207   2.5445   2.8055  17.983   100</code></pre>
 </div>
 <p>It is very astonishing that <code>phyper()</code> is hundreds of
 times faster than <code>fisher.test()</code>. Main reason is in
@@ -1001,7 +1001,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb38">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1625,7 +1625,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 76867,320214,23797,110355,217011,103583</code></pre>
+<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 20317,622554,21681,105988,67000,239731</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 mmu04913                                       Ovarian steroidogenesis - Mus musculus (house mouse)
 mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
          GeneRatio BgRatio       pvalue     p.adjust       qvalue
-mmu00590    16/454 85/9392 2.456998e-06 0.0007542983 0.0006620963
-mmu00565    11/454 48/9392 1.327107e-05 0.0014975168 0.0013144670
-mmu00592     8/454 25/9392 1.463371e-05 0.0014975168 0.0013144670
-mmu00591    11/454 50/9392 2.009867e-05 0.0015425732 0.0013540159
-mmu04913    12/454 63/9392 3.956222e-05 0.0024291201 0.0021321953
-mmu04061    14/454 95/9392 1.740468e-04 0.0079696743 0.0069954967
+mmu00590    16/454 85/9408 2.403809e-06 0.0007379694 0.0006452329
+mmu00565    11/454 48/9408 1.306159e-05 0.0014791271 0.0012932536
+mmu00592     8/454 25/9408 1.445401e-05 0.0014791271 0.0012932536
+mmu00591    11/454 50/9408 1.978440e-05 0.0015184527 0.0013276373
+mmu04913    12/454 63/9408 3.891349e-05 0.0023892882 0.0020890399
+mmu04061    14/454 95/9408 1.710081e-04 0.0078109667 0.0068294068
                                                                                                        geneID
 mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
 mmu00565                               18783/211429/329502/78390/22239/18781/18784/232889/320981/237625/53897
@@ -2647,7 +2647,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/07-gene-set-analysis.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/08-next-steps.html b/08-next-steps.html
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       </div>
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         <h1>Next steps</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/08-next-steps.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
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   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/08-next-steps.html",
   "dateCreated": "2020-09-15",
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         <h1>Contributor Code of Conduct</h1>
-        <p> Last updated on 2023-11-21 | 
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         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
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   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
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+        <p> Last updated on 2024-01-02 | 
         
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   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/LICENSE.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
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  [1] hgu95av2.db_3.13.0          org.Hs.eg.db_3.17.0        
  [3] org.Mm.eg.db_3.17.0         AnnotationDbi_1.62.2       
  [5] SummarizedExperiment_1.30.2 Biobase_2.60.0             
- [7] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+ [7] MatrixGenerics_1.12.3       matrixStats_1.2.0          
  [9] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [11] IRanges_2.34.1              S4Vectors_0.38.2           
 [13] BiocGenerics_0.46.0         knitr_1.45                 
 
 loaded via a namespace (and not attached):
- [1] Matrix_1.6-1.1          bit_4.0.5               highr_0.10             
+ [1] Matrix_1.6-4            bit_4.0.5               highr_0.10             
  [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.3             
  [7] crayon_1.5.2            blob_1.2.4              Biostrings_2.68.1      
 [10] bitops_1.0-7            png_0.1-8               fastmap_1.1.1          
-[13] yaml_2.3.7              lattice_0.22-5          R6_2.5.1               
+[13] yaml_2.3.8              lattice_0.22-5          R6_2.5.1               
 [16] XVector_0.40.0          S4Arrays_1.0.6          DelayedArray_0.26.7    
-[19] GenomeInfoDbData_1.2.10 DBI_1.1.3               rlang_1.1.2            
+[19] GenomeInfoDbData_1.2.10 DBI_1.2.0               rlang_1.1.2            
 [22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.41              
-[25] bit64_4.0.5             RSQLite_2.3.3           memoise_2.0.1          
-[28] cli_3.6.1               zlibbioc_1.46.0         grid_4.3.2             
-[31] vctrs_0.6.4             evaluate_0.23           abind_1.4-5            
+[25] bit64_4.0.5             RSQLite_2.3.4           memoise_2.0.1          
+[28] cli_3.6.2               zlibbioc_1.46.0         grid_4.3.2             
+[31] vctrs_0.6.5             evaluate_0.23           abind_1.4-5            
 [34] RCurl_1.98-1.13         httr_1.4.7              pkgconfig_2.0.3        
 [37] tools_4.3.2            </code></pre>
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  [5] ComplexHeatmap_2.16.0       ggplot2_3.4.4              
  [7] vsn_3.68.0                  DESeq2_1.40.2              
  [9] SummarizedExperiment_1.30.2 Biobase_2.60.0             
-[11] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+[11] MatrixGenerics_1.12.3       matrixStats_1.2.0          
 [13] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [15] IRanges_2.34.1              S4Vectors_0.38.2           
 [17] BiocGenerics_0.46.0        
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 loaded via a namespace (and not attached):
  [1] bitops_1.0-7            rlang_1.1.2             magrittr_2.0.3         
  [4] shinydashboard_0.7.2    clue_0.3-65             GetoptLong_1.0.5       
- [7] compiler_4.3.2          mgcv_1.9-0              png_0.1-8              
-[10] vctrs_0.6.4             pkgconfig_2.0.3         shape_1.4.6            
+ [7] compiler_4.3.2          mgcv_1.9-1              png_0.1-8              
+[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6            
 [13] crayon_1.5.2            fastmap_1.1.1           XVector_0.40.0         
 [16] ellipsis_0.3.2          labeling_0.4.3          utf8_1.2.4             
 [19] promises_1.2.1          preprocessCore_1.62.1   shinyAce_0.4.2         
 [22] xfun_0.41               cachem_1.0.8            zlibbioc_1.46.0        
-[25] jsonlite_1.8.7          highr_0.10              later_1.3.1            
+[25] jsonlite_1.8.8          highr_0.10              later_1.3.2            
 [28] DelayedArray_0.26.7     BiocParallel_1.34.2     parallel_4.3.2         
-[31] cluster_2.1.4           R6_2.5.1                bslib_0.5.1            
+[31] cluster_2.1.6           R6_2.5.1                bslib_0.6.1            
 [34] limma_3.56.2            jquerylib_0.1.4         Rcpp_1.0.11            
-[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.12          
-[40] Matrix_1.6-1.1          splines_4.3.2           igraph_1.5.1           
-[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.7             
+[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.13          
+[40] Matrix_1.6-4            splines_4.3.2           igraph_1.6.0           
+[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.8             
 [46] doParallel_1.0.17       codetools_0.2-19        affy_1.78.2            
 [49] miniUI_0.1.1.1          lattice_0.22-5          tibble_3.2.1           
-[52] shiny_1.7.5.1           withr_2.5.2             evaluate_0.23          
+[52] shiny_1.8.0             withr_2.5.2             evaluate_0.23          
 [55] circlize_0.4.15         pillar_1.9.0            affyio_1.70.0          
-[58] BiocManager_1.30.22     renv_1.0.3              DT_0.30                
+[58] BiocManager_1.30.22     renv_1.0.3              DT_0.31                
 [61] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3         
-[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.2.1           
+[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.3.0           
 [67] xtable_1.8-4            glue_1.6.2              tools_4.3.2            
 [70] colourpicker_1.3.0      locfit_1.5-9.8          colorspace_2.1-0       
-[73] nlme_3.1-163            GenomeInfoDbData_1.2.10 vipor_0.4.5            
-[76] cli_3.6.1               fansi_1.0.5             viridisLite_0.4.2      
-[79] S4Arrays_1.0.6          dplyr_1.1.3             gtable_0.3.4           
-[82] rintrojs_0.3.3          sass_0.4.7              digest_0.6.33          
+[73] nlme_3.1-164            GenomeInfoDbData_1.2.10 vipor_0.4.7            
+[76] cli_3.6.2               fansi_1.0.6             viridisLite_0.4.2      
+[79] S4Arrays_1.0.6          dplyr_1.1.4             gtable_0.3.4           
+[82] rintrojs_0.3.3          sass_0.4.8              digest_0.6.33          
 [85] ggrepel_0.9.4           farver_2.1.1            rjson_0.2.21           
-[88] htmlwidgets_1.6.2       htmltools_0.5.7         lifecycle_1.0.3        
+[88] htmlwidgets_1.6.4       htmltools_0.5.7         lifecycle_1.0.4        
 [91] shinyWidgets_0.8.0      GlobalOptions_0.1.2     mime_0.12              </code></pre>
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 <pre class="output" tabindex="0"><code>Unit: microseconds
-   expr     min      lq      mean   median       uq     max neval
- fisher 238.465 243.715 252.68149 246.8705 252.3760 488.411   100
-  hyper   1.352   1.543   2.23699   2.5545   2.8355   5.901   100</code></pre>
+   expr     min       lq      mean   median       uq     max neval
+ fisher 238.455 241.8405 250.98679 244.1705 251.2475 552.429   100
+  hyper   1.332   1.5180   2.38207   2.5445   2.8055  17.983   100</code></pre>
 </div>
 <p>It is very astonishing that <code>phyper()</code> is hundreds of
 times faster than <code>fisher.test()</code>. Main reason is in
@@ -5886,7 +5886,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb38">
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@@ -6545,7 +6545,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 76867,320214,23797,110355,217011,103583</code></pre>
+<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 20317,622554,21681,105988,67000,239731</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6823,12 +6823,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mmu04913                                       Ovarian steroidogenesis - Mus musculus (house mouse)
 mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
          GeneRatio BgRatio       pvalue     p.adjust       qvalue
-mmu00590    16/454 85/9392 2.456998e-06 0.0007542983 0.0006620963
-mmu00565    11/454 48/9392 1.327107e-05 0.0014975168 0.0013144670
-mmu00592     8/454 25/9392 1.463371e-05 0.0014975168 0.0013144670
-mmu00591    11/454 50/9392 2.009867e-05 0.0015425732 0.0013540159
-mmu04913    12/454 63/9392 3.956222e-05 0.0024291201 0.0021321953
-mmu04061    14/454 95/9392 1.740468e-04 0.0079696743 0.0069954967
+mmu00590    16/454 85/9408 2.403809e-06 0.0007379694 0.0006452329
+mmu00565    11/454 48/9408 1.306159e-05 0.0014791271 0.0012932536
+mmu00592     8/454 25/9408 1.445401e-05 0.0014791271 0.0012932536
+mmu00591    11/454 50/9408 1.978440e-05 0.0015184527 0.0013276373
+mmu04913    12/454 63/9408 3.891349e-05 0.0023892882 0.0020890399
+mmu04061    14/454 95/9408 1.710081e-04 0.0078109667 0.0068294068
                                                                                                        geneID
 mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
 mmu00565                               18783/211429/329502/78390/22239/18781/18784/232889/320981/237625/53897
@@ -7549,7 +7549,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </ol>
 </div></section><section id="aio-08-next-steps"><p>Content from <a href="08-next-steps.html">Next steps</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/08-next-steps.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
diff --git a/discuss.html b/discuss.html
index 90ba1cf1..86ecf245 100644
--- a/discuss.html
+++ b/discuss.html
@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -339,7 +339,7 @@ <h1>Discussion</h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/discuss.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png
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diff --git a/fig/07-gene-set-analysis-rendered-hypergeom-1.png b/fig/07-gene-set-analysis-rendered-hypergeom-1.png
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diff --git a/instructor/01-intro-to-rnaseq.html b/instructor/01-intro-to-rnaseq.html
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@@ -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 RNA-seq</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/01-intro-to-rnaseq.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -663,7 +663,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/01-intro-to-rnaseq.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/02-setup.html b/instructor/02-setup.html
index 5375786a..05b0eb69 100644
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@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>RStudio Project and Experimental Data</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/02-setup.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -655,7 +655,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/02-setup.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/03-import-annotate.html b/instructor/03-import-annotate.html
index cd240003..c6c942fe 100644
--- a/instructor/03-import-annotate.html
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@@ -288,7 +288,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Importing and annotating quantified data into R</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/03-import-annotate.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -526,7 +526,7 @@ <h3 class="callout-title">Challenge: Discuss the following points with
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li>In <code>counts</code>, the rows are genes just like the rows in
 <code>rowranges</code>. The columns in <code>counts</code> are the
@@ -646,7 +646,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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@@ -1023,7 +1023,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
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@@ -1150,7 +1150,7 @@ <h3 class="callout-title">Challenge: How to subset to mRNA genes<a class="anchor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 <div class="codewrapper sourceCode" id="cb55">
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@@ -1334,23 +1334,23 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [1] hgu95av2.db_3.13.0          org.Hs.eg.db_3.17.0        
  [3] org.Mm.eg.db_3.17.0         AnnotationDbi_1.62.2       
  [5] SummarizedExperiment_1.30.2 Biobase_2.60.0             
- [7] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+ [7] MatrixGenerics_1.12.3       matrixStats_1.2.0          
  [9] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [11] IRanges_2.34.1              S4Vectors_0.38.2           
 [13] BiocGenerics_0.46.0         knitr_1.45                 
 
 loaded via a namespace (and not attached):
- [1] Matrix_1.6-1.1          bit_4.0.5               highr_0.10             
+ [1] Matrix_1.6-4            bit_4.0.5               highr_0.10             
  [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.3             
  [7] crayon_1.5.2            blob_1.2.4              Biostrings_2.68.1      
 [10] bitops_1.0-7            png_0.1-8               fastmap_1.1.1          
-[13] yaml_2.3.7              lattice_0.22-5          R6_2.5.1               
+[13] yaml_2.3.8              lattice_0.22-5          R6_2.5.1               
 [16] XVector_0.40.0          S4Arrays_1.0.6          DelayedArray_0.26.7    
-[19] GenomeInfoDbData_1.2.10 DBI_1.1.3               rlang_1.1.2            
+[19] GenomeInfoDbData_1.2.10 DBI_1.2.0               rlang_1.1.2            
 [22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.41              
-[25] bit64_4.0.5             RSQLite_2.3.3           memoise_2.0.1          
-[28] cli_3.6.1               zlibbioc_1.46.0         grid_4.3.2             
-[31] vctrs_0.6.4             evaluate_0.23           abind_1.4-5            
+[25] bit64_4.0.5             RSQLite_2.3.4           memoise_2.0.1          
+[28] cli_3.6.2               zlibbioc_1.46.0         grid_4.3.2             
+[31] vctrs_0.6.5             evaluate_0.23           abind_1.4-5            
 [34] RCurl_1.98-1.13         httr_1.4.7              pkgconfig_2.0.3        
 [37] tools_4.3.2            </code></pre>
 </div>
@@ -1426,7 +1426,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/03-import-annotate.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/04-exploratory-qc.html b/instructor/04-exploratory-qc.html
index 860e6d09..c35c2f98 100644
--- a/instructor/04-exploratory-qc.html
+++ b/instructor/04-exploratory-qc.html
@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Exploratory analysis and quality control</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/04-exploratory-qc.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -836,7 +836,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [5] ComplexHeatmap_2.16.0       ggplot2_3.4.4              
  [7] vsn_3.68.0                  DESeq2_1.40.2              
  [9] SummarizedExperiment_1.30.2 Biobase_2.60.0             
-[11] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+[11] MatrixGenerics_1.12.3       matrixStats_1.2.0          
 [13] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [15] IRanges_2.34.1              S4Vectors_0.38.2           
 [17] BiocGenerics_0.46.0        
@@ -844,34 +844,34 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
  [1] bitops_1.0-7            rlang_1.1.2             magrittr_2.0.3         
  [4] shinydashboard_0.7.2    clue_0.3-65             GetoptLong_1.0.5       
- [7] compiler_4.3.2          mgcv_1.9-0              png_0.1-8              
-[10] vctrs_0.6.4             pkgconfig_2.0.3         shape_1.4.6            
+ [7] compiler_4.3.2          mgcv_1.9-1              png_0.1-8              
+[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6            
 [13] crayon_1.5.2            fastmap_1.1.1           XVector_0.40.0         
 [16] ellipsis_0.3.2          labeling_0.4.3          utf8_1.2.4             
 [19] promises_1.2.1          preprocessCore_1.62.1   shinyAce_0.4.2         
 [22] xfun_0.41               cachem_1.0.8            zlibbioc_1.46.0        
-[25] jsonlite_1.8.7          highr_0.10              later_1.3.1            
+[25] jsonlite_1.8.8          highr_0.10              later_1.3.2            
 [28] DelayedArray_0.26.7     BiocParallel_1.34.2     parallel_4.3.2         
-[31] cluster_2.1.4           R6_2.5.1                bslib_0.5.1            
+[31] cluster_2.1.6           R6_2.5.1                bslib_0.6.1            
 [34] limma_3.56.2            jquerylib_0.1.4         Rcpp_1.0.11            
-[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.12          
-[40] Matrix_1.6-1.1          splines_4.3.2           igraph_1.5.1           
-[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.7             
+[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.13          
+[40] Matrix_1.6-4            splines_4.3.2           igraph_1.6.0           
+[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.8             
 [46] doParallel_1.0.17       codetools_0.2-19        affy_1.78.2            
 [49] miniUI_0.1.1.1          lattice_0.22-5          tibble_3.2.1           
-[52] shiny_1.7.5.1           withr_2.5.2             evaluate_0.23          
+[52] shiny_1.8.0             withr_2.5.2             evaluate_0.23          
 [55] circlize_0.4.15         pillar_1.9.0            affyio_1.70.0          
-[58] BiocManager_1.30.22     renv_1.0.3              DT_0.30                
+[58] BiocManager_1.30.22     renv_1.0.3              DT_0.31                
 [61] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3         
-[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.2.1           
+[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.3.0           
 [67] xtable_1.8-4            glue_1.6.2              tools_4.3.2            
 [70] colourpicker_1.3.0      locfit_1.5-9.8          colorspace_2.1-0       
-[73] nlme_3.1-163            GenomeInfoDbData_1.2.10 vipor_0.4.5            
-[76] cli_3.6.1               fansi_1.0.5             viridisLite_0.4.2      
-[79] S4Arrays_1.0.6          dplyr_1.1.3             gtable_0.3.4           
-[82] rintrojs_0.3.3          sass_0.4.7              digest_0.6.33          
+[73] nlme_3.1-164            GenomeInfoDbData_1.2.10 vipor_0.4.7            
+[76] cli_3.6.2               fansi_1.0.6             viridisLite_0.4.2      
+[79] S4Arrays_1.0.6          dplyr_1.1.4             gtable_0.3.4           
+[82] rintrojs_0.3.3          sass_0.4.8              digest_0.6.33          
 [85] ggrepel_0.9.4           farver_2.1.1            rjson_0.2.21           
-[88] htmlwidgets_1.6.2       htmltools_0.5.7         lifecycle_1.0.3        
+[88] htmlwidgets_1.6.4       htmltools_0.5.7         lifecycle_1.0.4        
 [91] shinyWidgets_0.8.0      GlobalOptions_0.1.2     mime_0.12              </code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
@@ -946,7 +946,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/04-exploratory-qc.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/05-differential-expression.html b/instructor/05-differential-expression.html
index 10dfb3c2..665586b3 100644
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@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Differential expression analysis</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/05-differential-expression.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -1092,7 +1092,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/05-differential-expression.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/06-extra-design.html b/instructor/06-extra-design.html
index ff217b7d..982f0094 100644
--- a/instructor/06-extra-design.html
+++ b/instructor/06-extra-design.html
@@ -291,7 +291,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Extra exploration of design matrices</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/06-extra-design.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -659,7 +659,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -746,7 +746,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2001,7 +2001,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/06-extra-design.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/07-gene-set-analysis.html b/instructor/07-gene-set-analysis.html
index c8558bbb..bc379f98 100644
--- a/instructor/07-gene-set-analysis.html
+++ b/instructor/07-gene-set-analysis.html
@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Gene set enrichment analysis</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/07-gene-set-analysis.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -844,9 +844,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>Unit: microseconds
-   expr     min      lq      mean   median       uq     max neval
- fisher 238.465 243.715 252.68149 246.8705 252.3760 488.411   100
-  hyper   1.352   1.543   2.23699   2.5545   2.8355   5.901   100</code></pre>
+   expr     min       lq      mean   median       uq     max neval
+ fisher 238.455 241.8405 250.98679 244.1705 251.2475 552.429   100
+  hyper   1.332   1.5180   2.38207   2.5445   2.8055  17.983   100</code></pre>
 </div>
 <p>It is very astonishing that <code>phyper()</code> is hundreds of
 times faster than <code>fisher.test()</code>. Main reason is in
@@ -1003,7 +1003,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb38">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1627,7 +1627,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 76867,320214,23797,110355,217011,103583</code></pre>
+<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 20317,622554,21681,105988,67000,239731</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1898,12 +1898,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mmu04913                                       Ovarian steroidogenesis - Mus musculus (house mouse)
 mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
          GeneRatio BgRatio       pvalue     p.adjust       qvalue
-mmu00590    16/454 85/9392 2.456998e-06 0.0007542983 0.0006620963
-mmu00565    11/454 48/9392 1.327107e-05 0.0014975168 0.0013144670
-mmu00592     8/454 25/9392 1.463371e-05 0.0014975168 0.0013144670
-mmu00591    11/454 50/9392 2.009867e-05 0.0015425732 0.0013540159
-mmu04913    12/454 63/9392 3.956222e-05 0.0024291201 0.0021321953
-mmu04061    14/454 95/9392 1.740468e-04 0.0079696743 0.0069954967
+mmu00590    16/454 85/9408 2.403809e-06 0.0007379694 0.0006452329
+mmu00565    11/454 48/9408 1.306159e-05 0.0014791271 0.0012932536
+mmu00592     8/454 25/9408 1.445401e-05 0.0014791271 0.0012932536
+mmu00591    11/454 50/9408 1.978440e-05 0.0015184527 0.0013276373
+mmu04913    12/454 63/9408 3.891349e-05 0.0023892882 0.0020890399
+mmu04061    14/454 95/9408 1.710081e-04 0.0078109667 0.0068294068
                                                                                                        geneID
 mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
 mmu00565                               18783/211429/329502/78390/22239/18781/18784/232889/320981/237625/53897
@@ -2649,7 +2649,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/07-gene-set-analysis.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/08-next-steps.html b/instructor/08-next-steps.html
index 5e337b54..53666cd4 100644
--- a/instructor/08-next-steps.html
+++ b/instructor/08-next-steps.html
@@ -283,7 +283,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Next steps</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/08-next-steps.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -435,7 +435,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/08-next-steps.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 5025abff..976bab8b 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -271,7 +271,7 @@ <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 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -348,7 +348,7 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index e3f22897..82c00c92 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -271,7 +271,7 @@ <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 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -399,7 +399,7 @@ <h1>Licenses</h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/LICENSE.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/aio.html b/instructor/aio.html
index 79c38c27..a3ce2f48 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -337,7 +337,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-01-intro-to-rnaseq"><p>Content from <a href="01-intro-to-rnaseq.html">Introduction to RNA-seq</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/01-intro-to-rnaseq.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> 100 minutes </p>
@@ -685,7 +685,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </div></section><section id="aio-02-setup"><p>Content from <a href="02-setup.html">RStudio Project and Experimental Data</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/02-setup.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>
@@ -1027,7 +1027,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-03-import-annotate"><p>Content from <a href="03-import-annotate.html">Importing and annotating quantified data into R</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/03-import-annotate.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> 120 minutes </p>
@@ -1269,7 +1269,7 @@ <h3 class="callout-title">Challenge: Discuss the following points with
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li>In <code>counts</code>, the rows are genes just like the rows in
@@ -1396,7 +1396,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
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@@ -1775,7 +1775,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb46">
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@@ -1904,7 +1904,7 @@ <h3 class="callout-title">Challenge: How to subset to mRNA genes<a class="anchor
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb55">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2095,23 +2095,23 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [1] hgu95av2.db_3.13.0          org.Hs.eg.db_3.17.0        
  [3] org.Mm.eg.db_3.17.0         AnnotationDbi_1.62.2       
  [5] SummarizedExperiment_1.30.2 Biobase_2.60.0             
- [7] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+ [7] MatrixGenerics_1.12.3       matrixStats_1.2.0          
  [9] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [11] IRanges_2.34.1              S4Vectors_0.38.2           
 [13] BiocGenerics_0.46.0         knitr_1.45                 
 
 loaded via a namespace (and not attached):
- [1] Matrix_1.6-1.1          bit_4.0.5               highr_0.10             
+ [1] Matrix_1.6-4            bit_4.0.5               highr_0.10             
  [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.3             
  [7] crayon_1.5.2            blob_1.2.4              Biostrings_2.68.1      
 [10] bitops_1.0-7            png_0.1-8               fastmap_1.1.1          
-[13] yaml_2.3.7              lattice_0.22-5          R6_2.5.1               
+[13] yaml_2.3.8              lattice_0.22-5          R6_2.5.1               
 [16] XVector_0.40.0          S4Arrays_1.0.6          DelayedArray_0.26.7    
-[19] GenomeInfoDbData_1.2.10 DBI_1.1.3               rlang_1.1.2            
+[19] GenomeInfoDbData_1.2.10 DBI_1.2.0               rlang_1.1.2            
 [22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.41              
-[25] bit64_4.0.5             RSQLite_2.3.3           memoise_2.0.1          
-[28] cli_3.6.1               zlibbioc_1.46.0         grid_4.3.2             
-[31] vctrs_0.6.4             evaluate_0.23           abind_1.4-5            
+[25] bit64_4.0.5             RSQLite_2.3.4           memoise_2.0.1          
+[28] cli_3.6.2               zlibbioc_1.46.0         grid_4.3.2             
+[31] vctrs_0.6.5             evaluate_0.23           abind_1.4-5            
 [34] RCurl_1.98-1.13         httr_1.4.7              pkgconfig_2.0.3        
 [37] tools_4.3.2            </code></pre>
 </div>
@@ -2137,7 +2137,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-exploratory-qc"><p>Content from <a href="04-exploratory-qc.html">Exploratory analysis and quality control</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/04-exploratory-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> 180 minutes </p>
@@ -2706,7 +2706,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
  [5] ComplexHeatmap_2.16.0       ggplot2_3.4.4              
  [7] vsn_3.68.0                  DESeq2_1.40.2              
  [9] SummarizedExperiment_1.30.2 Biobase_2.60.0             
-[11] MatrixGenerics_1.12.3       matrixStats_1.0.0          
+[11] MatrixGenerics_1.12.3       matrixStats_1.2.0          
 [13] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [15] IRanges_2.34.1              S4Vectors_0.38.2           
 [17] BiocGenerics_0.46.0        
@@ -2714,34 +2714,34 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 loaded via a namespace (and not attached):
  [1] bitops_1.0-7            rlang_1.1.2             magrittr_2.0.3         
  [4] shinydashboard_0.7.2    clue_0.3-65             GetoptLong_1.0.5       
- [7] compiler_4.3.2          mgcv_1.9-0              png_0.1-8              
-[10] vctrs_0.6.4             pkgconfig_2.0.3         shape_1.4.6            
+ [7] compiler_4.3.2          mgcv_1.9-1              png_0.1-8              
+[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6            
 [13] crayon_1.5.2            fastmap_1.1.1           XVector_0.40.0         
 [16] ellipsis_0.3.2          labeling_0.4.3          utf8_1.2.4             
 [19] promises_1.2.1          preprocessCore_1.62.1   shinyAce_0.4.2         
 [22] xfun_0.41               cachem_1.0.8            zlibbioc_1.46.0        
-[25] jsonlite_1.8.7          highr_0.10              later_1.3.1            
+[25] jsonlite_1.8.8          highr_0.10              later_1.3.2            
 [28] DelayedArray_0.26.7     BiocParallel_1.34.2     parallel_4.3.2         
-[31] cluster_2.1.4           R6_2.5.1                bslib_0.5.1            
+[31] cluster_2.1.6           R6_2.5.1                bslib_0.6.1            
 [34] limma_3.56.2            jquerylib_0.1.4         Rcpp_1.0.11            
-[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.12          
-[40] Matrix_1.6-1.1          splines_4.3.2           igraph_1.5.1           
-[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.7             
+[37] iterators_1.0.14        knitr_1.45              httpuv_1.6.13          
+[40] Matrix_1.6-4            splines_4.3.2           igraph_1.6.0           
+[43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.8             
 [46] doParallel_1.0.17       codetools_0.2-19        affy_1.78.2            
 [49] miniUI_0.1.1.1          lattice_0.22-5          tibble_3.2.1           
-[52] shiny_1.7.5.1           withr_2.5.2             evaluate_0.23          
+[52] shiny_1.8.0             withr_2.5.2             evaluate_0.23          
 [55] circlize_0.4.15         pillar_1.9.0            affyio_1.70.0          
-[58] BiocManager_1.30.22     renv_1.0.3              DT_0.30                
+[58] BiocManager_1.30.22     renv_1.0.3              DT_0.31                
 [61] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3         
-[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.2.1           
+[64] RCurl_1.98-1.13         munsell_0.5.0           scales_1.3.0           
 [67] xtable_1.8-4            glue_1.6.2              tools_4.3.2            
 [70] colourpicker_1.3.0      locfit_1.5-9.8          colorspace_2.1-0       
-[73] nlme_3.1-163            GenomeInfoDbData_1.2.10 vipor_0.4.5            
-[76] cli_3.6.1               fansi_1.0.5             viridisLite_0.4.2      
-[79] S4Arrays_1.0.6          dplyr_1.1.3             gtable_0.3.4           
-[82] rintrojs_0.3.3          sass_0.4.7              digest_0.6.33          
+[73] nlme_3.1-164            GenomeInfoDbData_1.2.10 vipor_0.4.7            
+[76] cli_3.6.2               fansi_1.0.6             viridisLite_0.4.2      
+[79] S4Arrays_1.0.6          dplyr_1.1.4             gtable_0.3.4           
+[82] rintrojs_0.3.3          sass_0.4.8              digest_0.6.33          
 [85] ggrepel_0.9.4           farver_2.1.1            rjson_0.2.21           
-[88] htmlwidgets_1.6.2       htmltools_0.5.7         lifecycle_1.0.3        
+[88] htmlwidgets_1.6.4       htmltools_0.5.7         lifecycle_1.0.4        
 [91] shinyWidgets_0.8.0      GlobalOptions_0.1.2     mime_0.12              </code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
@@ -2766,7 +2766,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-05-differential-expression"><p>Content from <a href="05-differential-expression.html">Differential expression analysis</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/05-differential-expression.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> 105 minutes </p>
@@ -3532,7 +3532,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-06-extra-design"><p>Content from <a href="06-extra-design.html">Extra exploration of design matrices</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/06-extra-design.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> 60 minutes </p>
@@ -3899,7 +3899,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3987,7 +3987,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5200,7 +5200,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-07-gene-set-analysis"><p>Content from <a href="07-gene-set-analysis.html">Gene set enrichment analysis</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/07-gene-set-analysis.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> 105 minutes </p>
@@ -5798,9 +5798,9 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
 <pre class="output" tabindex="0"><code>Unit: microseconds
-   expr     min      lq      mean   median       uq     max neval
- fisher 238.465 243.715 252.68149 246.8705 252.3760 488.411   100
-  hyper   1.352   1.543   2.23699   2.5545   2.8355   5.901   100</code></pre>
+   expr     min       lq      mean   median       uq     max neval
+ fisher 238.455 241.8405 250.98679 244.1705 251.2475 552.429   100
+  hyper   1.332   1.5180   2.38207   2.5445   2.8055  17.983   100</code></pre>
 </div>
 <p>It is very astonishing that <code>phyper()</code> is hundreds of
 times faster than <code>fisher.test()</code>. Main reason is in
@@ -5960,7 +5960,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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@@ -6619,7 +6619,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 76867,320214,23797,110355,217011,103583</code></pre>
+<pre class="output" tabindex="0"><code>--&gt; Expected input gene ID: 20317,622554,21681,105988,67000,239731</code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6897,12 +6897,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 mmu04913                                       Ovarian steroidogenesis - Mus musculus (house mouse)
 mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
          GeneRatio BgRatio       pvalue     p.adjust       qvalue
-mmu00590    16/454 85/9392 2.456998e-06 0.0007542983 0.0006620963
-mmu00565    11/454 48/9392 1.327107e-05 0.0014975168 0.0013144670
-mmu00592     8/454 25/9392 1.463371e-05 0.0014975168 0.0013144670
-mmu00591    11/454 50/9392 2.009867e-05 0.0015425732 0.0013540159
-mmu04913    12/454 63/9392 3.956222e-05 0.0024291201 0.0021321953
-mmu04061    14/454 95/9392 1.740468e-04 0.0079696743 0.0069954967
+mmu00590    16/454 85/9408 2.403809e-06 0.0007379694 0.0006452329
+mmu00565    11/454 48/9408 1.306159e-05 0.0014791271 0.0012932536
+mmu00592     8/454 25/9408 1.445401e-05 0.0014791271 0.0012932536
+mmu00591    11/454 50/9408 1.978440e-05 0.0015184527 0.0013276373
+mmu04913    12/454 63/9408 3.891349e-05 0.0023892882 0.0020890399
+mmu04061    14/454 95/9408 1.710081e-04 0.0078109667 0.0068294068
                                                                                                        geneID
 mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
 mmu00565                               18783/211429/329502/78390/22239/18781/18784/232889/320981/237625/53897
@@ -7623,7 +7623,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </ol>
 </div></section><section id="aio-08-next-steps"><p>Content from <a href="08-next-steps.html">Next steps</a></p>
 <hr>
-<p> Last updated on 2023-11-21 | 
+<p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/episodes/08-next-steps.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> 20 minutes </p>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index 8e656805..d9bb015e 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -341,7 +341,7 @@ <h1>Discussion</h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/discuss.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
 }
 
diff --git a/instructor/reference.html b/instructor/reference.html
index 31a6f3c6..d5cf026f 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1></h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -341,7 +341,7 @@ <h1></h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/instructor/reference.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
   "datePublished": "2024-01-02"
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diff --git a/pkgdown.yml b/pkgdown.yml
index 8edacb84..6d33ed95 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.19.2
 pkgdown: 2.0.7
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-last_built: 2024-01-02T01:14Z
+last_built: 2024-01-02T07:58Z
 
diff --git a/reference.html b/reference.html
index 301ec802..2de021de 100644
--- a/reference.html
+++ b/reference.html
@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1></h1>
-        <p> Last updated on 2023-11-21 | 
+        <p> Last updated on 2024-01-02 | 
         
         <a href="https://github.com/carpentries-incubator/bioc-rnaseq/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -339,7 +339,7 @@ <h1></h1>
   "url": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-rnaseq/reference.html",
   "dateCreated": "2020-09-15",
-  "dateModified": "2023-11-21",
+  "dateModified": "2024-01-02",
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