From 40b71e1dcfe18e78e24e89a466f45dfcc241ed29 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 19 Mar 2024 01:04:28 +0000
Subject: [PATCH] site deploy

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Source  : 4187a380cecdcaa82b1aab45f303c43f4f7f3ecd
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Author  : GitHub Actions <actions@github.com>
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Message : markdown source builds

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Source  : 522aa3d1f1f01c9c59ecdb127cf784517507467d
Branch  : main
Author  : The Carpentries Apprentice (beta) <64428345+carpentries-bot@users.noreply.github.com>
Time    : 2023-11-07 14:42:01 +0000
Message : [actions] update 23 packages (#76)

Co-authored-by: zkamvar <zkamvar@users.noreply.github.com>
---
 01-setup.html                                 |  11 +-
 02-introduction-to-bioconductor.html          |  39 +++---
 03-installing-bioconductor.html               |  39 +++---
 04-getting-help.html                          |  25 ++--
 05-s4.html                                    |  25 ++--
 06-biological-sequences.html                  |  11 +-
 07-genomic-ranges.html                        |  25 ++--
 404.html                                      |   6 +-
 CODE_OF_CONDUCT.html                          |   4 +-
 LICENSE.html                                  |   4 +-
 aio.html                                      | 132 +++++++++---------
 discuss.html                                  |   4 +-
 images.html                                   |   6 +-
 index.html                                    |   6 +-
 instructor-notes.html                         |   6 +-
 instructor/01-setup.html                      |  11 +-
 .../02-introduction-to-bioconductor.html      |  39 +++---
 instructor/03-installing-bioconductor.html    |  39 +++---
 instructor/04-getting-help.html               |  25 ++--
 instructor/05-s4.html                         |  25 ++--
 instructor/06-biological-sequences.html       |  11 +-
 instructor/07-genomic-ranges.html             |  25 ++--
 instructor/404.html                           |   6 +-
 instructor/CODE_OF_CONDUCT.html               |   4 +-
 instructor/LICENSE.html                       |   4 +-
 instructor/aio.html                           | 132 +++++++++---------
 instructor/discuss.html                       |   4 +-
 instructor/images.html                        |   6 +-
 instructor/index.html                         |   6 +-
 instructor/instructor-notes.html              |   6 +-
 instructor/key-points.html                    |   6 +-
 instructor/profiles.html                      |   6 +-
 instructor/reference.html                     |   4 +-
 key-points.html                               |   6 +-
 pkgdown.yml                                   |   2 +-
 profiles.html                                 |   6 +-
 reference.html                                |   4 +-
 renv.lock                                     |   2 +-
 38 files changed, 382 insertions(+), 340 deletions(-)

diff --git a/01-setup.html b/01-setup.html
index d361159a..31df173a 100644
--- a/01-setup.html
+++ b/01-setup.html
@@ -362,12 +362,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    destfile <span class="op">=</span> <span class="st">"data/actb_orfs.fasta"</span></span>
 <span><span class="op">)</span></span></code></pre>
 </div>
-<div id="callout1" class="callout">
+<div id="note" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>Ideally, participants might want to create a new <a href="https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects" class="external-link">RStudio
 project</a> and download the lesson files in a sub-directory of that
@@ -431,7 +432,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -454,7 +455,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/01-setup.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/02-introduction-to-bioconductor.html b/02-introduction-to-bioconductor.html
index 4755b7eb..956a5424 100644
--- a/02-introduction-to-bioconductor.html
+++ b/02-introduction-to-bioconductor.html
@@ -387,12 +387,13 @@ <h4 id="overview-and-relationship-to-cran">Overview and relationship to CRAN<a c
 – much larger and general-purpose in scope – to comprise R packages
 primarily catering for bioinformatics and computational biology
 analyses.</p>
-<div id="callout1" class="callout">
+<div id="going-further" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#bioconductor-and-CRAN">Discussion</a>
 article of this lesson includes a section discussing the relationship of
@@ -583,12 +584,13 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </div>
 </div>
 </div>
-<div id="callout2" class="callout">
+<div id="going-further-1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>The Bioconductor package <em><a href="https://bioconductor.org/packages/3.17/biocViews" class="external-link">biocViews</a></em>
 is used to support and manage the infrastructure of the controlled
@@ -649,12 +651,13 @@ <h3 id="conferences-courses-and-workshops">Conferences, courses and workshops<a
 used to publish video recordings of conference presentations including
 talks and workshops, as well as editions of the regular Bioconductor
 developers forum (link needed).</p>
-<div id="callout3" class="callout">
+<div id="contribute" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="contribute">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a></h3>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
+</h3>
 <div class="callout-content">
 <p>It could be great to illustrate a typical cycle of conferences over a
 year, e.g.</p>
@@ -690,12 +693,13 @@ <h4 id="slack-workspace">Slack workspace<a class="anchor" aria-label="anchor" hr
 channels of create new ones to discuss new subjects.</p>
 <p>Important announcements are posted on the <code>#general</code>
 channel.</p>
-<div id="callout4" class="callout">
+<div id="note" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>Users are encouraged to use the Bioconductor <a href="https://support.bioconductor.org/" class="external-link">support site</a> to raise
 issues that are relevant to the wider community. The Slack workspace is
@@ -733,12 +737,13 @@ <h3 id="a-scientific-and-technical-community">A scientific and technical communi
 Culhane (chair), Matt Ritchie (co Chair), Lori Kern (Secretary).</li>
 <li><a href="https://www.bioconductor.org/about/code-of-conduct/" class="external-link">Code
 of Conduct committee</a></li>
-</ul><div id="callout5" class="callout">
+</ul><div id="note-1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a></h3>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>At least 1 member of TAB/CAB sits on both to act at the liason to
 ensure communication of the board.</p>
@@ -826,7 +831,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -849,7 +854,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/02-introduction-to-bioconductor.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/03-installing-bioconductor.html b/03-installing-bioconductor.html
index baa38d1a..88ed7a32 100644
--- a/03-installing-bioconductor.html
+++ b/03-installing-bioconductor.html
@@ -362,12 +362,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 The downloaded binary packages are in
 	/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T//RtmpeS8MHV/downloaded_packages</code></pre>
 </div>
-<div id="callout1" class="callout">
+<div id="going-further" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>A number of packages that are not part of the base R installation
 also provide functions to install packages from various repositories.
@@ -466,12 +467,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>This needs to be done only once, as the <em><a href="https://bioconductor.org/packages/3.17/BiocVersion" class="external-link">BiocVersion</a></em>
 package will be updated to the corresponding version, indicating the
 version of Bioconductor in use in this R library.</p>
-<div id="callout2" class="callout">
+<div id="going-further-1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#the-bioconductor-release-cycle">Discussion</a>
 article of this lesson includes a section discussing the release cycle
@@ -553,12 +555,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Conveniently, if any package can be updated, the function generates
 and displays the command needed to update those packages. Users simply
 need to copy-paste and run that command in their R console.</p>
-<div id="callout3" class="callout">
+<div id="example-of-out-of-date-package-library" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="example-of-out-of-date-package-library">Example of out-of-date package library<a class="anchor" aria-label="anchor" href="#example-of-out-of-date-package-library"></a></h3>
+<div id="example-of-out-of-date-package-library" class="callout-inner">
+<h3 class="callout-title">Example of out-of-date package library<a class="anchor" aria-label="anchor" href="#example-of-out-of-date-package-library"></a>
+</h3>
 <div class="callout-content">
 <p>In the example below, the <code>BiocManager::valid()</code> function
 did not return <code>TRUE</code>. Instead, it includes information about
@@ -664,12 +667,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Each repository URL can be accessed in a web browser, displaying the
 full list of packages available from that repository. For instance,
 navigate to <a href="https://bioconductor.org/packages/3.14/bioc" class="external-link">https://bioconductor.org/packages/3.14/bioc</a>.</p>
-<div id="callout4" class="callout">
+<div id="going-further-2" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further-2">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a></h3>
+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+</h3>
 <div class="callout-content">
 <p>The function <code>BiocManager::repositories()</code> can be combined
 with the base function <code>available.packages()</code> to query
@@ -724,12 +728,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>However, if any package cannot be found in the Bioconductor
 repository, the function also searches for those packages in
 repositories listed in the global option <code>repos</code>.</p>
-<div id="callout5" class="callout">
+<div id="contribute" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="contribute">Contribute !<a class="anchor" aria-label="anchor" href="#contribute"></a></h3>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute !<a class="anchor" aria-label="anchor" href="#contribute"></a>
+</h3>
 <div class="callout-content">
 <p>Add an example of non-Bioconductor package that can be installed
 using BioManager. Preferably, a package that will be used later in this
@@ -811,7 +816,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -834,7 +839,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/04-getting-help.html b/04-getting-help.html
index e8102cec..a561136e 100644
--- a/04-getting-help.html
+++ b/04-getting-help.html
@@ -387,12 +387,13 @@ <h3 class="card-title">Objectives</h3>
 <p>In the “Details” section of the landing page, many packages provide a
 field labelled “BugReports”. That field provides a URL that users can
 visit to report bugs to the package developer(s).</p>
-<div id="callout1" class="callout">
+<div id="note" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>It can be difficult to distinguish actual software bugs from
 unwitting mistakes made by users not fully familiar with the package
@@ -411,12 +412,13 @@ <h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" hr
 dependencies indicating the number of other Bioconductor packages that
 must be installed before the package itself can be installed and used on
 the user’s system.</p>
-<div id="callout2" class="callout">
+<div id="going-further" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>Each package has a landing page for each release of Bioconductor
 since the package was added to the repository, e.g.:</p>
@@ -552,12 +554,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 (e.g., diversity and representation).</p>
 <p>Private channels also exist for governance (e.g., event organisation,
 advisory boards).</p>
-<div id="callout3" class="callout">
+<div id="note-1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a></h3>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>The Slack workspace allows for rapid day-to-day communication and
 discussion with fellow community members through channels and direct
@@ -674,7 +677,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -697,7 +700,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/04-getting-help.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/05-s4.html b/05-s4.html
index fbb8363e..0e158db3 100644
--- a/05-s4.html
+++ b/05-s4.html
@@ -539,12 +539,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
     expand.grid, I, unname</code></pre>
 </div>
-<div id="callout1" class="callout">
+<div id="note" class="callout">
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 </div>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>The package startup messages printed in the console are worth noting
 that the <em><a href="https://bioconductor.org/packages/3.17/S4Vectors" class="external-link">S4Vectors</a></em>
@@ -931,12 +932,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 Letters    character         3
 Floats        double         3</code></pre>
 </div>
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-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a></h3>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>The row names of the metadata columns are automatically set to match
 the column names of the parent <code>DataFrame</code>, clearly
@@ -1040,12 +1042,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 9          2     2  TRUE
 10         2     2  TRUE</code></pre>
 </div>
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 <i class="callout-icon" data-feather="bell"></i>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>A number of standard operations with <code>Rle</code> objects are
 documented in the help page of the <code>Rle</code> class, accessible as
@@ -1114,7 +1117,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -1137,7 +1140,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/05-s4.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/06-biological-sequences.html b/06-biological-sequences.html
index 6881d062..37ee8070 100644
--- a/06-biological-sequences.html
+++ b/06-biological-sequences.html
@@ -619,12 +619,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [5]    34 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT                PE2
 [6]    34 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC                PE2_rc</code></pre>
 </div>
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>The help page of the function <code>readDNAStringSet()</code> –
 accessible using <code>help(readDNAStringSet)</code> – documents related
@@ -926,7 +927,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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 		</footer></div> <!-- / div.container -->
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@@ -949,7 +950,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/06-biological-sequences.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/07-genomic-ranges.html b/07-genomic-ranges.html
index 3e683fbe..b3888270 100644
--- a/07-genomic-ranges.html
+++ b/07-genomic-ranges.html
@@ -731,12 +731,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In this example, we confirm that the first range in the query set
 overlaps the first range in the subject set; while the second range in
 the query set overlaps both ranges in the subject set.</p>
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>For downstream use, the two components can be extracted from
 <code>Hits</code> objects using their names, respectively:</p>
@@ -1019,12 +1020,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths</code></pre>
 </div>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>Individual methods for parsing specific file formats can be invoked
 directly. For instance, in this case, the GTF file format being
@@ -1326,12 +1328,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In the example above, we learn that the new <code>GRanges</code>
 object has 11 records less than the original <code>GRanges</code>
 object.</p>
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+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+</h3>
 <div class="callout-content">
 <p>Many more methods exist to operate on <code>GRanges</code> and
 <code>GRangesList</code> objects than what could be demonstrated
@@ -1399,7 +1402,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -1422,7 +1425,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/07-genomic-ranges.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 292a9a6e..a36b2b74 100644
--- a/404.html
+++ b/404.html
@@ -305,7 +305,7 @@ <h1>Page not found</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -327,8 +327,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/404.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/404.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index cc30134e..200b2a4e 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -322,7 +322,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -345,7 +345,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 90d32ace..644dff50 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -374,7 +374,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
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@@ -397,7 +397,7 @@ <h1>Licenses</h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/LICENSE.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index d2630c0c..c8029257 100644
--- a/aio.html
+++ b/aio.html
@@ -405,12 +405,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    destfile <span class="op">=</span> <span class="st">"data/actb_orfs.fasta"</span></span>
 <span><span class="op">)</span></span></code></pre>
 </div>
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 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
 </h3>
 <div class="callout-content">
 <p>Ideally, participants might want to create a new <a href="https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects" class="external-link">RStudio
@@ -556,12 +556,12 @@ <h4 id="overview-and-relationship-to-cran">Overview and relationship to CRAN<a c
 – much larger and general-purpose in scope – to comprise R packages
 primarily catering for bioinformatics and computational biology
 analyses.</p>
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+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
 </h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#bioconductor-and-CRAN">Discussion</a>
@@ -768,12 +768,12 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </div>
 </div>
 </div>
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 </div>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
 </h3>
 <div class="callout-content">
 <p>The Bioconductor package <em><a href="https://bioconductor.org/packages/3.17/biocViews" class="external-link">biocViews</a></em>
@@ -839,12 +839,12 @@ <h3 id="conferences-courses-and-workshops">Conferences, courses and workshops<a
 used to publish video recordings of conference presentations including
 talks and workshops, as well as editions of the regular Bioconductor
 developers forum (link needed).</p>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="contribute">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
 </h3>
 <div class="callout-content">
 <p>It could be great to illustrate a typical cycle of conferences over a
@@ -888,12 +888,12 @@ <h4 id="slack-workspace">Slack workspace<a class="anchor" aria-label="anchor" hr
 channels of create new ones to discuss new subjects.</p>
 <p>Important announcements are posted on the <code>#general</code>
 channel.</p>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
 </h3>
 <div class="callout-content">
 <p>Users are encouraged to use the Bioconductor <a href="https://support.bioconductor.org/" class="external-link">support site</a> to raise
@@ -936,12 +936,12 @@ <h3 id="a-scientific-and-technical-community">A scientific and technical communi
 <li><a href="https://www.bioconductor.org/about/code-of-conduct/" class="external-link">Code
 of Conduct committee</a></li>
 </ul>
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 <p>This needs to be done only once, as the <em><a href="https://bioconductor.org/packages/3.17/BiocVersion" class="external-link">BiocVersion</a></em>
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     expand.grid, I, unname</code></pre>
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 Letters    character         3
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 9          2     2  TRUE
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 [5]    34 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT                PE2
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 <p>In this example, we confirm that the first range in the query set
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   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths</code></pre>
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 <p>In the example above, we learn that the new <code>GRanges</code>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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   "identifier": "https://carpentries-incubator.github.io/bioc-project/aio.html",
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-  "dateModified": "2024-03-12",
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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   "identifier": "https://carpentries-incubator.github.io/bioc-project/discuss.html",
   "dateCreated": "2020-09-14",
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@@ -386,7 +386,7 @@ <h3 id="07-genomic-ranges-figure-3">Figure 3</h3>
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   "url": "https://carpentries-incubator.github.io/bioc-project/images.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/images.html",
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-  "dateModified": "2024-03-12",
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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   "url": "https://carpentries-incubator.github.io/bioc-project/index.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/index.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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   "url": "https://carpentries-incubator.github.io/bioc-project/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor-notes.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
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diff --git a/instructor/01-setup.html b/instructor/01-setup.html
index 8e140a3c..44faf31f 100644
--- a/instructor/01-setup.html
+++ b/instructor/01-setup.html
@@ -364,12 +364,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    destfile <span class="op">=</span> <span class="st">"data/actb_orfs.fasta"</span></span>
 <span><span class="op">)</span></span></code></pre>
 </div>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>Ideally, participants might want to create a new <a href="https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects" class="external-link">RStudio
 project</a> and download the lesson files in a sub-directory of that
@@ -433,7 +434,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -456,7 +457,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/01-setup.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/02-introduction-to-bioconductor.html b/instructor/02-introduction-to-bioconductor.html
index f76b43e4..6dc508f0 100644
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+++ b/instructor/02-introduction-to-bioconductor.html
@@ -389,12 +389,13 @@ <h4 id="overview-and-relationship-to-cran">Overview and relationship to CRAN<a c
 – much larger and general-purpose in scope – to comprise R packages
 primarily catering for bioinformatics and computational biology
 analyses.</p>
-<div id="callout1" class="callout">
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#bioconductor-and-CRAN">Discussion</a>
 article of this lesson includes a section discussing the relationship of
@@ -585,12 +586,13 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </div>
 </div>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>The Bioconductor package <em><a href="https://bioconductor.org/packages/3.17/biocViews" class="external-link">biocViews</a></em>
 is used to support and manage the infrastructure of the controlled
@@ -651,12 +653,13 @@ <h3 id="conferences-courses-and-workshops">Conferences, courses and workshops<a
 used to publish video recordings of conference presentations including
 talks and workshops, as well as editions of the regular Bioconductor
 developers forum (link needed).</p>
-<div id="callout3" class="callout">
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="contribute">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a></h3>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
+</h3>
 <div class="callout-content">
 <p>It could be great to illustrate a typical cycle of conferences over a
 year, e.g.</p>
@@ -692,12 +695,13 @@ <h4 id="slack-workspace">Slack workspace<a class="anchor" aria-label="anchor" hr
 channels of create new ones to discuss new subjects.</p>
 <p>Important announcements are posted on the <code>#general</code>
 channel.</p>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h3>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>Users are encouraged to use the Bioconductor <a href="https://support.bioconductor.org/" class="external-link">support site</a> to raise
 issues that are relevant to the wider community. The Slack workspace is
@@ -735,12 +739,13 @@ <h3 id="a-scientific-and-technical-community">A scientific and technical communi
 Culhane (chair), Matt Ritchie (co Chair), Lori Kern (Secretary).</li>
 <li><a href="https://www.bioconductor.org/about/code-of-conduct/" class="external-link">Code
 of Conduct committee</a></li>
-</ul><div id="callout5" class="callout">
+</ul><div id="note-1" class="callout">
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-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a></h3>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>At least 1 member of TAB/CAB sits on both to act at the liason to
 ensure communication of the board.</p>
@@ -828,7 +833,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -851,7 +856,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/02-introduction-to-bioconductor.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
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   </script><script>
diff --git a/instructor/03-installing-bioconductor.html b/instructor/03-installing-bioconductor.html
index 1a7d6cde..4f2830e0 100644
--- a/instructor/03-installing-bioconductor.html
+++ b/instructor/03-installing-bioconductor.html
@@ -364,12 +364,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 The downloaded binary packages are in
 	/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T//RtmpeS8MHV/downloaded_packages</code></pre>
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+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
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 <p>A number of packages that are not part of the base R installation
 also provide functions to install packages from various repositories.
@@ -468,12 +469,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>This needs to be done only once, as the <em><a href="https://bioconductor.org/packages/3.17/BiocVersion" class="external-link">BiocVersion</a></em>
 package will be updated to the corresponding version, indicating the
 version of Bioconductor in use in this R library.</p>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#the-bioconductor-release-cycle">Discussion</a>
 article of this lesson includes a section discussing the release cycle
@@ -555,12 +557,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Conveniently, if any package can be updated, the function generates
 and displays the command needed to update those packages. Users simply
 need to copy-paste and run that command in their R console.</p>
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+<div id="example-of-out-of-date-package-library" class="callout-inner">
+<h3 class="callout-title">Example of out-of-date package library<a class="anchor" aria-label="anchor" href="#example-of-out-of-date-package-library"></a>
+</h3>
 <div class="callout-content">
 <p>In the example below, the <code>BiocManager::valid()</code> function
 did not return <code>TRUE</code>. Instead, it includes information about
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 <p>Each repository URL can be accessed in a web browser, displaying the
 full list of packages available from that repository. For instance,
 navigate to <a href="https://bioconductor.org/packages/3.14/bioc" class="external-link">https://bioconductor.org/packages/3.14/bioc</a>.</p>
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-<h3 class="callout-title" id="going-further-2">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a></h3>
+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+</h3>
 <div class="callout-content">
 <p>The function <code>BiocManager::repositories()</code> can be combined
 with the base function <code>available.packages()</code> to query
@@ -726,12 +730,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>However, if any package cannot be found in the Bioconductor
 repository, the function also searches for those packages in
 repositories listed in the global option <code>repos</code>.</p>
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+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute !<a class="anchor" aria-label="anchor" href="#contribute"></a>
+</h3>
 <div class="callout-content">
 <p>Add an example of non-Bioconductor package that can be installed
 using BioManager. Preferably, a package that will be used later in this
@@ -813,7 +818,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/03-installing-bioconductor.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
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@@ -389,12 +389,13 @@ <h3 class="card-title">Objectives</h3>
 <p>In the “Details” section of the landing page, many packages provide a
 field labelled “BugReports”. That field provides a URL that users can
 visit to report bugs to the package developer(s).</p>
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+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
 <div class="callout-content">
 <p>It can be difficult to distinguish actual software bugs from
 unwitting mistakes made by users not fully familiar with the package
@@ -413,12 +414,13 @@ <h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" hr
 dependencies indicating the number of other Bioconductor packages that
 must be installed before the package itself can be installed and used on
 the user’s system.</p>
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>Each package has a landing page for each release of Bioconductor
 since the package was added to the repository, e.g.:</p>
@@ -554,12 +556,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 (e.g., diversity and representation).</p>
 <p>Private channels also exist for governance (e.g., event organisation,
 advisory boards).</p>
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+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>The Slack workspace allows for rapid day-to-day communication and
 discussion with fellow community members through channels and direct
@@ -676,7 +679,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -699,7 +702,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/04-getting-help.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
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     expand.grid, I, unname</code></pre>
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+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+</h3>
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 <p>The package startup messages printed in the console are worth noting
 that the <em><a href="https://bioconductor.org/packages/3.17/S4Vectors" class="external-link">S4Vectors</a></em>
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 Letters    character         3
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+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+</h3>
 <div class="callout-content">
 <p>The row names of the metadata columns are automatically set to match
 the column names of the parent <code>DataFrame</code>, clearly
@@ -1042,12 +1044,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 9          2     2  TRUE
 10         2     2  TRUE</code></pre>
 </div>
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 <i class="callout-icon" data-feather="bell"></i>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>A number of standard operations with <code>Rle</code> objects are
 documented in the help page of the <code>Rle</code> class, accessible as
@@ -1116,7 +1119,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -1139,7 +1142,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/05-s4.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/06-biological-sequences.html b/instructor/06-biological-sequences.html
index 6550d99c..d3708710 100644
--- a/instructor/06-biological-sequences.html
+++ b/instructor/06-biological-sequences.html
@@ -621,12 +621,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [5]    34 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT                PE2
 [6]    34 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC                PE2_rc</code></pre>
 </div>
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 <i class="callout-icon" data-feather="bell"></i>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a></h3>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>The help page of the function <code>readDNAStringSet()</code> –
 accessible using <code>help(readDNAStringSet)</code> – documents related
@@ -928,7 +929,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -951,7 +952,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/06-biological-sequences.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/07-genomic-ranges.html b/instructor/07-genomic-ranges.html
index e8185331..81d8bdc6 100644
--- a/instructor/07-genomic-ranges.html
+++ b/instructor/07-genomic-ranges.html
@@ -733,12 +733,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In this example, we confirm that the first range in the query set
 overlaps the first range in the subject set; while the second range in
 the query set overlaps both ranges in the subject set.</p>
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+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+</h3>
 <div class="callout-content">
 <p>For downstream use, the two components can be extracted from
 <code>Hits</code> objects using their names, respectively:</p>
@@ -1021,12 +1022,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths</code></pre>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a></h3>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+</h3>
 <div class="callout-content">
 <p>Individual methods for parsing specific file formats can be invoked
 directly. For instance, in this case, the GTF file format being
@@ -1328,12 +1330,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In the example above, we learn that the new <code>GRanges</code>
 object has 11 records less than the original <code>GRanges</code>
 object.</p>
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-<h3 class="callout-title" id="going-further-2">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a></h3>
+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+</h3>
 <div class="callout-content">
 <p>Many more methods exist to operate on <code>GRanges</code> and
 <code>GRangesList</code> objects than what could be demonstrated
@@ -1401,7 +1404,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/07-genomic-ranges.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 82e55c7b..4dc0c7b1 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -305,7 +305,7 @@ <h1>Page not found</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -327,8 +327,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/404.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/404.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 51dda6f9..3f9b1cdd 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -324,7 +324,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
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@@ -347,7 +347,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index f73e9c62..3cb606b8 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -376,7 +376,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
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@@ -399,7 +399,7 @@ <h1>Licenses</h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/LICENSE.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 5bab2fdd..75fcb147 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -408,12 +408,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>    destfile <span class="op">=</span> <span class="st">"data/actb_orfs.fasta"</span></span>
 <span><span class="op">)</span></span></code></pre>
 </div>
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 </div>
-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
 </h3>
 <div class="callout-content">
 <p>Ideally, participants might want to create a new <a href="https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects" class="external-link">RStudio
@@ -560,12 +560,12 @@ <h4 id="overview-and-relationship-to-cran">Overview and relationship to CRAN<a c
 – much larger and general-purpose in scope – to comprise R packages
 primarily catering for bioinformatics and computational biology
 analyses.</p>
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+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
 </h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#bioconductor-and-CRAN">Discussion</a>
@@ -772,12 +772,12 @@ <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </div>
 </div>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
 </h3>
 <div class="callout-content">
 <p>The Bioconductor package <em><a href="https://bioconductor.org/packages/3.17/biocViews" class="external-link">biocViews</a></em>
@@ -843,12 +843,12 @@ <h3 id="conferences-courses-and-workshops">Conferences, courses and workshops<a
 used to publish video recordings of conference presentations including
 talks and workshops, as well as editions of the regular Bioconductor
 developers forum (link needed).</p>
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-<h3 class="callout-title" id="contribute">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute!<a class="anchor" aria-label="anchor" href="#contribute"></a>
 </h3>
 <div class="callout-content">
 <p>It could be great to illustrate a typical cycle of conferences over a
@@ -892,12 +892,12 @@ <h4 id="slack-workspace">Slack workspace<a class="anchor" aria-label="anchor" hr
 channels of create new ones to discuss new subjects.</p>
 <p>Important announcements are posted on the <code>#general</code>
 channel.</p>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
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+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
 </h3>
 <div class="callout-content">
 <p>Users are encouraged to use the Bioconductor <a href="https://support.bioconductor.org/" class="external-link">support site</a> to raise
@@ -940,12 +940,12 @@ <h3 id="a-scientific-and-technical-community">A scientific and technical communi
 <li><a href="https://www.bioconductor.org/about/code-of-conduct/" class="external-link">Code
 of Conduct committee</a></li>
 </ul>
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-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
 </h3>
 <div class="callout-content">
 <p>At least 1 member of TAB/CAB sits on both to act at the liason to
@@ -1084,12 +1084,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 The downloaded binary packages are in
 	/var/folders/51/nz__2dx10yzd75rylr5cg2zc0000gq/T//RtmpeS8MHV/downloaded_packages</code></pre>
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+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
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 <div class="callout-content">
 <p>A number of packages that are not part of the base R installation
@@ -1192,12 +1192,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>This needs to be done only once, as the <em><a href="https://bioconductor.org/packages/3.17/BiocVersion" class="external-link">BiocVersion</a></em>
 package will be updated to the corresponding version, indicating the
 version of Bioconductor in use in this R library.</p>
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+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
 </h3>
 <div class="callout-content">
 <p>The <a href="discuss.html#the-bioconductor-release-cycle">Discussion</a>
@@ -1281,12 +1281,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Conveniently, if any package can be updated, the function generates
 and displays the command needed to update those packages. Users simply
 need to copy-paste and run that command in their R console.</p>
-<div id="callout3" class="callout">
+<div id="example-of-out-of-date-package-library" class="callout">
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+<div id="example-of-out-of-date-package-library" class="callout-inner">
+<h3 class="callout-title">Example of out-of-date package library<a class="anchor" aria-label="anchor" href="#example-of-out-of-date-package-library"></a>
 </h3>
 <div class="callout-content">
 <p>In the example below, the <code>BiocManager::valid()</code> function
@@ -1394,12 +1394,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>Each repository URL can be accessed in a web browser, displaying the
 full list of packages available from that repository. For instance,
 navigate to <a href="https://bioconductor.org/packages/3.14/bioc" class="external-link">https://bioconductor.org/packages/3.14/bioc</a>.</p>
-<div id="callout4" class="callout">
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-<h3 class="callout-title" id="going-further-2">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
 </h3>
 <div class="callout-content">
 <p>The function <code>BiocManager::repositories()</code> can be combined
@@ -1456,12 +1456,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>However, if any package cannot be found in the Bioconductor
 repository, the function also searches for those packages in
 repositories listed in the global option <code>repos</code>.</p>
-<div id="callout5" class="callout">
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-<h3 class="callout-title" id="contribute">Contribute !<a class="anchor" aria-label="anchor" href="#contribute"></a>
+<div id="contribute" class="callout-inner">
+<h3 class="callout-title">Contribute !<a class="anchor" aria-label="anchor" href="#contribute"></a>
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 <div class="callout-content">
 <p>Add an example of non-Bioconductor package that can be installed
@@ -1620,12 +1620,12 @@ <h3 class="card-title">Objectives</h3>
 <p>In the “Details” section of the landing page, many packages provide a
 field labelled “BugReports”. That field provides a URL that users can
 visit to report bugs to the package developer(s).</p>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
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 <div class="callout-content">
 <p>It can be difficult to distinguish actual software bugs from
@@ -1645,12 +1645,12 @@ <h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" hr
 dependencies indicating the number of other Bioconductor packages that
 must be installed before the package itself can be installed and used on
 the user’s system.</p>
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
 </h3>
 <div class="callout-content">
 <p>Each package has a landing page for each release of Bioconductor
@@ -1798,12 +1798,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 (e.g., diversity and representation).</p>
 <p>Private channels also exist for governance (e.g., event organisation,
 advisory boards).</p>
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-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
 </h3>
 <div class="callout-content">
 <p>The Slack workspace allows for rapid day-to-day communication and
@@ -2157,12 +2157,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
     expand.grid, I, unname</code></pre>
 </div>
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-<h3 class="callout-title" id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a>
+<div id="note" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note"></a>
 </h3>
 <div class="callout-content">
 <p>The package startup messages printed in the console are worth noting
@@ -2557,12 +2557,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 Letters    character         3
 Floats        double         3</code></pre>
 </div>
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-<h3 class="callout-title" id="note-1">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
+<div id="note-1" class="callout-inner">
+<h3 class="callout-title">Note<a class="anchor" aria-label="anchor" href="#note-1"></a>
 </h3>
 <div class="callout-content">
 <p>The row names of the metadata columns are automatically set to match
@@ -2671,12 +2671,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 9          2     2  TRUE
 10         2     2  TRUE</code></pre>
 </div>
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
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 <div class="callout-content">
 <p>A number of standard operations with <code>Rle</code> objects are
@@ -3061,12 +3061,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [5]    34 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT                PE2
 [6]    34 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC                PE2_rc</code></pre>
 </div>
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-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
 </h3>
 <div class="callout-content">
 <p>The help page of the function <code>readDNAStringSet()</code> –
@@ -3808,12 +3808,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In this example, we confirm that the first range in the query set
 overlaps the first range in the subject set; while the second range in
 the query set overlaps both ranges in the subject set.</p>
-<div id="callout1" class="callout">
+<div id="going-further" class="callout">
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-<div class="section level3 callout-title callout-inner">
-<h3 class="callout-title" id="going-further">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
+<div id="going-further" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further"></a>
 </h3>
 <div class="callout-content">
 <p>For downstream use, the two components can be extracted from
@@ -4102,12 +4102,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths</code></pre>
 </div>
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 </div>
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-<h3 class="callout-title" id="going-further-1">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
+<div id="going-further-1" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-1"></a>
 </h3>
 <div class="callout-content">
 <p>Individual methods for parsing specific file formats can be invoked
@@ -4415,12 +4415,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>In the example above, we learn that the new <code>GRanges</code>
 object has 11 records less than the original <code>GRanges</code>
 object.</p>
-<div id="callout3" class="callout">
+<div id="going-further-2" class="callout">
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-<h3 class="callout-title" id="going-further-2">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
+<div id="going-further-2" class="callout-inner">
+<h3 class="callout-title">Going further<a class="anchor" aria-label="anchor" href="#going-further-2"></a>
 </h3>
 <div class="callout-content">
 <p>Many more methods exist to operate on <code>GRanges</code> and
@@ -4480,7 +4480,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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index de99a862..ea740a68 100644
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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diff --git a/instructor/images.html b/instructor/images.html
index 7692941b..371958ad 100644
--- a/instructor/images.html
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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 	<div id="to-top">
@@ -455,8 +455,8 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 0d810f94..15e5f3fd 100644
--- a/instructor/instructor-notes.html
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@@ -368,7 +368,7 @@ <h1>Instructor Notes</h1>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -391,8 +391,8 @@ <h1>Instructor Notes</h1>
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 }
 
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index 725ddbda..8c62e426 100644
--- a/instructor/key-points.html
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@@ -432,7 +432,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
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@@ -455,8 +455,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/key-points.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index b5deb065..61fcaa15 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -274,7 +274,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -296,8 +296,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/instructor/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/profiles.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
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diff --git a/instructor/reference.html b/instructor/reference.html
index f97740c3..6e371a66 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -403,7 +403,7 @@ <h1></h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -426,7 +426,7 @@ <h1></h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/instructor/reference.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 6b98f8f5..83758d6a 100644
--- a/key-points.html
+++ b/key-points.html
@@ -430,7 +430,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -453,8 +453,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://carpentries-incubator.github.io/bioc-project/key-points.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/key-points.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
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diff --git a/pkgdown.yml b/pkgdown.yml
index 4559dd1f..272bac0e 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-03-12T01:30Z
+last_built: 2024-03-19T01:04Z
 
diff --git a/profiles.html b/profiles.html
index f03bc413..5cd7a1f4 100644
--- a/profiles.html
+++ b/profiles.html
@@ -274,7 +274,7 @@ <h1>Learner Profiles</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -296,8 +296,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/bioc-project/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/bioc-project/profiles.html",
   "dateCreated": "2020-09-14",
-  "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "dateModified": "2024-03-19",
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index b57ef4ff..7d93c19c 100644
--- a/reference.html
+++ b/reference.html
@@ -401,7 +401,7 @@ <h1></h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
         
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.2" class="external-link">sandpaper (0.16.2)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.3" class="external-link">sandpaper (0.16.3)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.4" class="external-link">pegboard (0.7.4)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.1" class="external-link">varnish (1.0.1)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -424,7 +424,7 @@ <h1></h1>
   "identifier": "https://carpentries-incubator.github.io/bioc-project/reference.html",
   "dateCreated": "2020-09-14",
   "dateModified": "2024-03-12",
-  "datePublished": "2024-03-12"
+  "datePublished": "2024-03-19"
 }
 
   </script><script>
diff --git a/renv.lock b/renv.lock
index 5e61704b..e6b75782 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.2",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "BioCsoft",