From d6baa5bb075eb7ddba8896539382598707c8105d Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 2 Apr 2024 09:04:34 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : e5c8496d4884761564fafc3fc92fd80122dbc828
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-04-02 09:04:17 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : d90b5a4f3f0ca34e4520e26f2fbf92da2107b56a
Branch  : main
Author  : The Carpentries Apprentice (beta) <64428345+carpentries-bot@users.noreply.github.com>
Time    : 2024-04-02 09:00:24 +0000
Message : [actions] update 31 packages (#77)

Co-authored-by: zkamvar <zkamvar@users.noreply.github.com>
---
 01-setup.html                                 |  4 +-
 02-introduction-to-bioconductor.html          |  8 +--
 03-installing-bioconductor.html               | 23 ++++----
 04-getting-help.html                          |  4 +-
 05-s4.html                                    |  8 +--
 06-biological-sequences.html                  | 12 ++---
 07-genomic-ranges.html                        |  8 +--
 CODE_OF_CONDUCT.html                          |  4 +-
 LICENSE.html                                  |  4 +-
 aio.html                                      | 53 +++++++++----------
 discuss.html                                  |  4 +-
 instructor/01-setup.html                      |  4 +-
 .../02-introduction-to-bioconductor.html      |  8 +--
 instructor/03-installing-bioconductor.html    | 23 ++++----
 instructor/04-getting-help.html               |  4 +-
 instructor/05-s4.html                         |  8 +--
 instructor/06-biological-sequences.html       | 12 ++---
 instructor/07-genomic-ranges.html             |  8 +--
 instructor/CODE_OF_CONDUCT.html               |  4 +-
 instructor/LICENSE.html                       |  4 +-
 instructor/aio.html                           | 53 +++++++++----------
 instructor/discuss.html                       |  4 +-
 instructor/reference.html                     |  4 +-
 md5sum.txt                                    | 34 ++++++------
 pkgdown.yml                                   |  2 +-
 reference.html                                |  4 +-
 26 files changed, 144 insertions(+), 164 deletions(-)

diff --git a/01-setup.html b/01-setup.html
index e1db60a0..a9ce8ea6 100644
--- a/01-setup.html
+++ b/01-setup.html
@@ -277,7 +277,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction and setup</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/01-setup.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -454,7 +454,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/01-setup.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/01-setup.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/02-introduction-to-bioconductor.html b/02-introduction-to-bioconductor.html
index e1f3ae6f..c35f570e 100644
--- a/02-introduction-to-bioconductor.html
+++ b/02-introduction-to-bioconductor.html
@@ -277,7 +277,7 @@ <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</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/02-introduction-to-bioconductor.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -498,7 +498,7 @@ <h3 class="callout-title">Challenge: The Bioconductor website<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>The following solution includes numbers that were valid at the time
 of writing (Bioconductor release 3.13); numbers will inevitably be
@@ -569,7 +569,7 @@ <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">
 <ol style="list-style-type: decimal"><li>
 <code>RNAseq</code>, <code>ChIPSeq</code>, <code>Epigenetics</code>,
@@ -853,7 +853,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/02-introduction-to-bioconductor.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/02-introduction-to-bioconductor.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/03-installing-bioconductor.html b/03-installing-bioconductor.html
index 6d74ce29..1ee102a4 100644
--- a/03-installing-bioconductor.html
+++ b/03-installing-bioconductor.html
@@ -281,7 +281,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Installing Bioconductor packages</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/03-installing-bioconductor.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -498,7 +498,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="warning" tabindex="0"><code>Warning: 26 packages out-of-date; 1 packages too new</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: 0 packages out-of-date; 1 packages too new</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>
@@ -531,24 +531,19 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
  [1] BiocManager_1.30.22 compiler_4.3.3      fastmap_1.1.1      
- [4] cli_3.6.1           htmltools_0.5.7     tools_4.3.3        
- [7] yaml_2.3.7          rmarkdown_2.25      knitr_1.45         
-[10] digest_0.6.33       xfun_0.41           rlang_1.1.2        
+ [4] cli_3.6.2           htmltools_0.5.8     tools_4.3.3        
+ [7] yaml_2.3.8          rmarkdown_2.26      knitr_1.45         
+[10] digest_0.6.35       xfun_0.43           rlang_1.1.3        
 [13] renv_1.0.5          evaluate_0.23      
 
 Bioconductor version '3.17'
 
-  * 26 packages out-of-date
+  * 0 packages out-of-date
   * 1 packages too new
 
 create a valid installation with
 
-  BiocManager::install(c(
-    "BH", "bookdown", "bslib", "cli", "cpp11", "curl", "digest", "glue",
-    "jsonlite", "lifecycle", "matrixStats", "Rcpp", "RCurl", "renv", "rlang",
-    "rmarkdown", "sass", "SparseArray", "stringi", "stringr", "timechange",
-    "tinytex", "vctrs", "xfun", "XML", "xml2", "yaml"
-  ), update = TRUE, ask = FALSE, force = TRUE)
+  BiocManager::install("SparseArray", update = TRUE, ask = FALSE, force = TRUE)
 
 more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date</code></pre>
 </div>
@@ -634,7 +629,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>[1] 24114</code></pre>
+<pre class="output" tabindex="0"><code>[1] 24198</code></pre>
 </div>
 <p>Specifically, the current Bioconductor and CRAN repositories can be
 displayed as follows.</p>
@@ -838,7 +833,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/04-getting-help.html b/04-getting-help.html
index 87957dfe..d3a8156d 100644
--- a/04-getting-help.html
+++ b/04-getting-help.html
@@ -284,7 +284,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Getting help</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/04-getting-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -699,7 +699,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/04-getting-help.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/04-getting-help.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/05-s4.html b/05-s4.html
index 3a058ccc..40a4b7d3 100644
--- a/05-s4.html
+++ b/05-s4.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>S4 classes in Bioconductor</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/05-s4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -727,7 +727,7 @@ <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">
 <pre><code>&gt; DF2["name1", ]
 DataFrame with 1 row and 3 columns
@@ -782,7 +782,7 @@ <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">
 <pre><code>&gt; DF3["a", ]
 DataFrame with 1 row and 3 columns
@@ -1139,7 +1139,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/05-s4.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/05-s4.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/06-biological-sequences.html b/06-biological-sequences.html
index ce7118af..acf42a5c 100644
--- a/06-biological-sequences.html
+++ b/06-biological-sequences.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>Working with biological sequences</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/06-biological-sequences.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -388,7 +388,7 @@ <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">
 <p>Yes, this is a valid DNA sequence using ambiguity codes defined in
 the <a href="https://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation" class="external-link">IUPAC</a>
@@ -577,7 +577,7 @@ <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">
 <p>The method <code>countPattern()</code> reports 3 hits, because the
 option <code>fixed = FALSE</code> allows the pattern <code>GM</code> to
@@ -714,7 +714,7 @@ <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">
 <pre><code>&gt; setdiff(AA_PROTEINOGENIC, AA_STANDARD)
 [1] "U" "O"</code></pre>
@@ -857,7 +857,7 @@ <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="#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">
 <pre><code><span><span class="fu">width</span><span class="op">(</span><span class="va">actb_aa</span><span class="op">)</span></span>
 <span><span class="co"># or</span></span>
@@ -949,7 +949,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/06-biological-sequences.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/06-biological-sequences.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/07-genomic-ranges.html b/07-genomic-ranges.html
index 006244c5..8b556f56 100644
--- a/07-genomic-ranges.html
+++ b/07-genomic-ranges.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>Working with genomics ranges</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/07-genomic-ranges.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -534,7 +534,7 @@ <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="cb5">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1230,7 +1230,7 @@ <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" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb51">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1424,7 +1424,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/07-genomic-ranges.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/07-genomic-ranges.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index e7d7d2ba..25db7944 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -265,7 +265,7 @@ <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 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -344,7 +344,7 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/LICENSE.html b/LICENSE.html
index 6f8219f0..3c9afb78 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -265,7 +265,7 @@ <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 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/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://carpentries-incubator.github.io/bioc-project/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/LICENSE.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/aio.html b/aio.html
index cfc7e66c..5ee6117f 100644
--- a/aio.html
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 <section id="aio-01-setup"><p>Content from <a href="01-setup.html">Introduction and setup</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/01-setup.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -443,7 +443,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/02-introduction-to-bioconductor.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -673,7 +673,7 @@ <h3 class="callout-title">Challenge: The Bioconductor website<a class="anchor" a
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>The following solution includes numbers that were valid at the time
 of writing (Bioconductor release 3.13); numbers will inevitably be
@@ -751,7 +751,7 @@ <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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 <li>
@@ -999,7 +999,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 </section></section><section id="aio-03-installing-bioconductor"><p>Content from <a href="03-installing-bioconductor.html">Installing Bioconductor packages</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
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 </h3>
-<pre class="warning" tabindex="0"><code>Warning: 26 packages out-of-date; 1 packages too new</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: 0 packages out-of-date; 1 packages too new</code></pre>
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@@ -1252,24 +1252,19 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
  [1] BiocManager_1.30.22 compiler_4.3.3      fastmap_1.1.1      
- [4] cli_3.6.1           htmltools_0.5.7     tools_4.3.3        
- [7] yaml_2.3.7          rmarkdown_2.25      knitr_1.45         
-[10] digest_0.6.33       xfun_0.41           rlang_1.1.2        
+ [4] cli_3.6.2           htmltools_0.5.8     tools_4.3.3        
+ [7] yaml_2.3.8          rmarkdown_2.26      knitr_1.45         
+[10] digest_0.6.35       xfun_0.43           rlang_1.1.3        
 [13] renv_1.0.5          evaluate_0.23      
 
 Bioconductor version '3.17'
 
-  * 26 packages out-of-date
+  * 0 packages out-of-date
   * 1 packages too new
 
 create a valid installation with
 
-  BiocManager::install(c(
-    "BH", "bookdown", "bslib", "cli", "cpp11", "curl", "digest", "glue",
-    "jsonlite", "lifecycle", "matrixStats", "Rcpp", "RCurl", "renv", "rlang",
-    "rmarkdown", "sass", "SparseArray", "stringi", "stringr", "timechange",
-    "tinytex", "vctrs", "xfun", "XML", "xml2", "yaml"
-  ), update = TRUE, ask = FALSE, force = TRUE)
+  BiocManager::install("SparseArray", update = TRUE, ask = FALSE, force = TRUE)
 
 more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date</code></pre>
 </div>
@@ -1356,7 +1351,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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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>[1] 24114</code></pre>
+<pre class="output" tabindex="0"><code>[1] 24198</code></pre>
 </div>
 <p>Specifically, the current Bioconductor and CRAN repositories can be
 displayed as follows.</p>
@@ -1508,7 +1503,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-getting-help"><p>Content from <a href="04-getting-help.html">Getting help</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
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 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/05-s4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -2341,7 +2336,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" 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">
 <pre><code>&gt; DF2["name1", ]
 DataFrame with 1 row and 3 columns
@@ -2396,7 +2391,7 @@ <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">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <pre><code>&gt; DF3["a", ]
 DataFrame with 1 row and 3 columns
@@ -2707,7 +2702,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-06-biological-sequences"><p>Content from <a href="06-biological-sequences.html">Working with biological sequences</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/06-biological-sequences.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -2818,7 +2813,7 @@ <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">
 <p>Yes, this is a valid DNA sequence using ambiguity codes defined in
 the <a href="https://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation" class="external-link">IUPAC</a>
@@ -3010,7 +3005,7 @@ <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">
 <div class="accordion-body">
 <p>The method <code>countPattern()</code> reports 3 hits, because the
 option <code>fixed = FALSE</code> allows the pattern <code>GM</code> to
@@ -3151,7 +3146,7 @@ <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">
 <pre><code>&gt; setdiff(AA_PROTEINOGENIC, AA_STANDARD)
 [1] "U" "O"</code></pre>
@@ -3295,7 +3290,7 @@ <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="#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">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <pre><code><span><span class="fu">width</span><span class="op">(</span><span class="va">actb_aa</span><span class="op">)</span></span>
 <span><span class="co"># or</span></span>
@@ -3333,7 +3328,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-07-genomic-ranges"><p>Content from <a href="07-genomic-ranges.html">Working with genomics ranges</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/07-genomic-ranges.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -3600,7 +3595,7 @@ <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">
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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diff --git a/discuss.html b/discuss.html
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+++ b/discuss.html
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       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -494,7 +494,7 @@ <h3 id="transition-between-devel-and-release---the-release-process">Transition b
   "url": "https://carpentries-incubator.github.io/bioc-project/discuss.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/discuss.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/01-setup.html b/instructor/01-setup.html
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       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction and setup</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/01-setup.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -456,7 +456,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/01-setup.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/01-setup.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/02-introduction-to-bioconductor.html b/instructor/02-introduction-to-bioconductor.html
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+++ b/instructor/02-introduction-to-bioconductor.html
@@ -277,7 +277,7 @@ <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</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/02-introduction-to-bioconductor.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -500,7 +500,7 @@ <h3 class="callout-title">Challenge: The Bioconductor website<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>The following solution includes numbers that were valid at the time
 of writing (Bioconductor release 3.13); numbers will inevitably be
@@ -571,7 +571,7 @@ <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">
 <ol style="list-style-type: decimal"><li>
 <code>RNAseq</code>, <code>ChIPSeq</code>, <code>Epigenetics</code>,
@@ -855,7 +855,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/02-introduction-to-bioconductor.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/02-introduction-to-bioconductor.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/03-installing-bioconductor.html b/instructor/03-installing-bioconductor.html
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@@ -281,7 +281,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Installing Bioconductor packages</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/03-installing-bioconductor.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -500,7 +500,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="warning" tabindex="0"><code>Warning: 26 packages out-of-date; 1 packages too new</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: 0 packages out-of-date; 1 packages too new</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>
@@ -533,24 +533,19 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
  [1] BiocManager_1.30.22 compiler_4.3.3      fastmap_1.1.1      
- [4] cli_3.6.1           htmltools_0.5.7     tools_4.3.3        
- [7] yaml_2.3.7          rmarkdown_2.25      knitr_1.45         
-[10] digest_0.6.33       xfun_0.41           rlang_1.1.2        
+ [4] cli_3.6.2           htmltools_0.5.8     tools_4.3.3        
+ [7] yaml_2.3.8          rmarkdown_2.26      knitr_1.45         
+[10] digest_0.6.35       xfun_0.43           rlang_1.1.3        
 [13] renv_1.0.5          evaluate_0.23      
 
 Bioconductor version '3.17'
 
-  * 26 packages out-of-date
+  * 0 packages out-of-date
   * 1 packages too new
 
 create a valid installation with
 
-  BiocManager::install(c(
-    "BH", "bookdown", "bslib", "cli", "cpp11", "curl", "digest", "glue",
-    "jsonlite", "lifecycle", "matrixStats", "Rcpp", "RCurl", "renv", "rlang",
-    "rmarkdown", "sass", "SparseArray", "stringi", "stringr", "timechange",
-    "tinytex", "vctrs", "xfun", "XML", "xml2", "yaml"
-  ), update = TRUE, ask = FALSE, force = TRUE)
+  BiocManager::install("SparseArray", update = TRUE, ask = FALSE, force = TRUE)
 
 more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date</code></pre>
 </div>
@@ -636,7 +631,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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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>[1] 24114</code></pre>
+<pre class="output" tabindex="0"><code>[1] 24198</code></pre>
 </div>
 <p>Specifically, the current Bioconductor and CRAN repositories can be
 displayed as follows.</p>
@@ -840,7 +835,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/03-installing-bioconductor.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/03-installing-bioconductor.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/04-getting-help.html b/instructor/04-getting-help.html
index 80d6390a..249b16e9 100644
--- a/instructor/04-getting-help.html
+++ b/instructor/04-getting-help.html
@@ -284,7 +284,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Getting help</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/04-getting-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -701,7 +701,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/04-getting-help.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/04-getting-help.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/05-s4.html b/instructor/05-s4.html
index f6ad0a03..40b3db53 100644
--- a/instructor/05-s4.html
+++ b/instructor/05-s4.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>S4 classes in Bioconductor</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/05-s4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -729,7 +729,7 @@ <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">
 <pre><code>&gt; DF2["name1", ]
 DataFrame with 1 row and 3 columns
@@ -784,7 +784,7 @@ <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">
 <pre><code>&gt; DF3["a", ]
 DataFrame with 1 row and 3 columns
@@ -1141,7 +1141,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/05-s4.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/05-s4.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/06-biological-sequences.html b/instructor/06-biological-sequences.html
index bded46a6..21062ae4 100644
--- a/instructor/06-biological-sequences.html
+++ b/instructor/06-biological-sequences.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>Working with biological sequences</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/06-biological-sequences.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -390,7 +390,7 @@ <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">
 <p>Yes, this is a valid DNA sequence using ambiguity codes defined in
 the <a href="https://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation" class="external-link">IUPAC</a>
@@ -579,7 +579,7 @@ <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">
 <p>The method <code>countPattern()</code> reports 3 hits, because the
 option <code>fixed = FALSE</code> allows the pattern <code>GM</code> to
@@ -716,7 +716,7 @@ <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">
 <pre><code>&gt; setdiff(AA_PROTEINOGENIC, AA_STANDARD)
 [1] "U" "O"</code></pre>
@@ -859,7 +859,7 @@ <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="#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">
 <pre><code><span><span class="fu">width</span><span class="op">(</span><span class="va">actb_aa</span><span class="op">)</span></span>
 <span><span class="co"># or</span></span>
@@ -951,7 +951,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/06-biological-sequences.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/06-biological-sequences.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/07-genomic-ranges.html b/instructor/07-genomic-ranges.html
index 9f6b358f..3987ac48 100644
--- a/instructor/07-genomic-ranges.html
+++ b/instructor/07-genomic-ranges.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>Working with genomics ranges</h1>
-        <p>Last updated on 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/07-genomic-ranges.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -536,7 +536,7 @@ <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="cb5">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1232,7 +1232,7 @@ <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" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb51">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1426,7 +1426,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/07-genomic-ranges.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/07-genomic-ranges.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 0164147e..f0e722af 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -265,7 +265,7 @@ <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 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -346,7 +346,7 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index c2dc1a47..ed7820ae 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -265,7 +265,7 @@ <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 2024-03-12 |
+        <p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/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://carpentries-incubator.github.io/bioc-project/instructor/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/LICENSE.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
+  "dateModified": "2024-04-02",
   "datePublished": "2024-04-02"
 }
 
diff --git a/instructor/aio.html b/instructor/aio.html
index 9e87fa43..5d63ac15 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -322,7 +322,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-01-setup"><p>Content from <a href="01-setup.html">Introduction and setup</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/01-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> NA minutes</p>
@@ -446,7 +446,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-02-introduction-to-bioconductor"><p>Content from <a href="02-introduction-to-bioconductor.html">Introduction to Bioconductor</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/02-introduction-to-bioconductor.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> NA minutes</p>
@@ -677,7 +677,7 @@ <h3 class="callout-title">Challenge: The Bioconductor website<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>The following solution includes numbers that were valid at the time
 of writing (Bioconductor release 3.13); numbers will inevitably be
@@ -755,7 +755,7 @@ <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">
 <ol style="list-style-type: decimal">
 <li>
@@ -1003,7 +1003,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-03-installing-bioconductor"><p>Content from <a href="03-installing-bioconductor.html">Installing Bioconductor packages</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/03-installing-bioconductor.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> NA minutes</p>
@@ -1224,7 +1224,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">WARNING<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="warning" tabindex="0"><code>Warning: 26 packages out-of-date; 1 packages too new</code></pre>
+<pre class="warning" tabindex="0"><code>Warning: 0 packages out-of-date; 1 packages too new</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>
@@ -1257,24 +1257,19 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 loaded via a namespace (and not attached):
  [1] BiocManager_1.30.22 compiler_4.3.3      fastmap_1.1.1      
- [4] cli_3.6.1           htmltools_0.5.7     tools_4.3.3        
- [7] yaml_2.3.7          rmarkdown_2.25      knitr_1.45         
-[10] digest_0.6.33       xfun_0.41           rlang_1.1.2        
+ [4] cli_3.6.2           htmltools_0.5.8     tools_4.3.3        
+ [7] yaml_2.3.8          rmarkdown_2.26      knitr_1.45         
+[10] digest_0.6.35       xfun_0.43           rlang_1.1.3        
 [13] renv_1.0.5          evaluate_0.23      
 
 Bioconductor version '3.17'
 
-  * 26 packages out-of-date
+  * 0 packages out-of-date
   * 1 packages too new
 
 create a valid installation with
 
-  BiocManager::install(c(
-    "BH", "bookdown", "bslib", "cli", "cpp11", "curl", "digest", "glue",
-    "jsonlite", "lifecycle", "matrixStats", "Rcpp", "RCurl", "renv", "rlang",
-    "rmarkdown", "sass", "SparseArray", "stringi", "stringr", "timechange",
-    "tinytex", "vctrs", "xfun", "XML", "xml2", "yaml"
-  ), update = TRUE, ask = FALSE, force = TRUE)
+  BiocManager::install("SparseArray", update = TRUE, ask = FALSE, force = TRUE)
 
 more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date</code></pre>
 </div>
@@ -1361,7 +1356,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code>[1] 24114</code></pre>
+<pre class="output" tabindex="0"><code>[1] 24198</code></pre>
 </div>
 <p>Specifically, the current Bioconductor and CRAN repositories can be
 displayed as follows.</p>
@@ -1513,7 +1508,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-getting-help"><p>Content from <a href="04-getting-help.html">Getting help</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/04-getting-help.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> NA minutes</p>
@@ -1892,7 +1887,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-05-s4"><p>Content from <a href="05-s4.html">S4 classes in Bioconductor</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
+<p>Last updated on 2024-04-02 |
         
         <a href="https://github.com/carpentries-incubator/bioc-project/edit/main/episodes/05-s4.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> NA minutes</p>
@@ -2348,7 +2343,7 @@ <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">
 <pre><code>&gt; DF2["name1", ]
 DataFrame with 1 row and 3 columns
@@ -2403,7 +2398,7 @@ <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">
 <pre><code>&gt; DF3["a", ]
 DataFrame with 1 row and 3 columns
@@ -2714,7 +2709,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-06-biological-sequences"><p>Content from <a href="06-biological-sequences.html">Working with biological sequences</a></p>
 <hr>
-<p>Last updated on 2024-03-12 |
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 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> NA minutes</p>
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