diff --git a/00-introduction.html b/00-introduction.html
index 5a068a08..b8b03dd0 100644
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+++ b/00-introduction.html
@@ -301,10 +301,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -324,7 +324,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
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-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -401,8 +401,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
-<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a></h2>
+<section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a></h2>
 <hr class="half-width"><p>In this lesson we will take you through the very first things you
 need to get R working.</p>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout">
@@ -410,8 +409,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anchor" aria-label="anchor" href="#tip-this-lesson-works-best-on-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: This lesson works best on the cloud</h3>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
 virtual machine instances provided to you at a genomics workshop. Much
@@ -423,16 +421,14 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
-<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a></h2>
+</section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a></h2>
 <hr class="half-width"><p><a href="https://en.wikipedia.org/wiki/R_(programming_language)" class="external-link">The
 programming language R</a> has been around since 1995, and was created
 by Ross Ihaka and Robert Gentleman at the University of Auckland, New
 Zealand. R is based off the S programming language developed at Bell
 Labs and was developed to teach intro statistics. See this <a href="https://www.stat.auckland.ac.nz/~ihaka/downloads/Massey.pdf" class="external-link">slide
 deck</a> by Ross Ihaka for more info on the subject.</p>
-</section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
-<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a></h2>
+</section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a></h2>
 <hr class="half-width"><p>At more than 20 years old, R is fairly mature and <a href="https://www.tiobe.com/tiobe-index/r/" class="external-link">growing in popularity</a>.
 However, programming isn’t a popularity contest. Here are key advantages
 of analyzing data in R:</p>
@@ -462,8 +458,7 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="discussion-your-experience" class="callout-inner">
-<h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-label="anchor" href="#discussion-your-experience"></a>
-</h3>
+<h3 class="callout-title">Discussion: Your experience</h3>
 <div class="callout-content">
 <p>What has motivated you to learn R? Have you had a research question
 for which spreadsheet programs such as Excel have proven difficult to
@@ -471,8 +466,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a></h2>
+</section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a></h2>
 <hr class="half-width"><p>In these lessons, we will be making use of a software called <a href="https://www.rstudio.com/products/RStudio/" class="external-link">RStudio</a>, an <a href="https://en.wikipedia.org/wiki/Integrated_development_environment" class="external-link">Integrated
 Development Environment (IDE)</a>. RStudio, like most IDEs, provides a
 graphical interface to R, making it more user-friendly, and providing
@@ -482,8 +476,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 Server</a>, a version of RStudio that can be accessed in your web
 browser. RStudio Server has the same features of the Desktop version of
 RStudio you could download as standalone software.</p>
-</section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a></h2>
+</section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a></h2>
 <hr class="half-width"><p>Open a web browser and enter the URL you used to log in at the
 terminal (provided by your instructors), followed by <code>:8787</code>.
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
@@ -494,8 +487,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout-inner">
-<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.<a class="anchor" aria-label="anchor" href="#tip-make-sure-there-are-no-spaces-before-or-after-your-url."></a>
-</h3>
+<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.</h3>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -508,8 +500,7 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 credentials for the genomics Data Carpentry instances will be provided
 by your instructors.</p>
 <p>You should now see the RStudio interface:</p>
-<figure><img src="fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
-<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a></h2>
+<figure><img src="fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a></h2>
 <hr class="half-width"><p>One of the first benefits we will take advantage of in RStudio is
 something called an <strong>RStudio Project</strong>. An RStudio project
 allows you to more easily:</p>
@@ -549,8 +540,7 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-your-project-more-reproducible-with-renv" class="callout-inner">
-<h3 class="callout-title">Tip: Make your project more reproducible with renv<a class="anchor" aria-label="anchor" href="#tip-make-your-project-more-reproducible-with-renv"></a>
-</h3>
+<h3 class="callout-title">Tip: Make your project more reproducible with renv</h3>
 <div class="callout-content">
 <p>One of the most wonderful and also frustrating aspects of working
 with R is managing packages. We will talk more about them, but packages
@@ -568,8 +558,7 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a>
-<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a></h2>
+</section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a></h2>
 <hr class="half-width"><p>Now that we are ready to start exploring R, we will want to keep a
 record of the commands we are using. To do this we can create an R
 script:</p>
@@ -587,16 +576,14 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-save-your-script-now" class="callout-inner">
-<h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label="anchor" href="#tip-save-your-script-now"></a>
-</h3>
+<h3 class="callout-title">Tip: Save your script now</h3>
 <div class="callout-content">
 <p>Remember to save your script at this point. Anything can happen
 during your lesson and you don’t want to lose your work!</p>
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a>
-<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a></h2>
+</section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a></h2>
 <hr class="half-width"><p>Here are the major windows (or panes) of the RStudio environment:</p>
 <figure><img src="fig/rstudio_session_4pane_layout.png" alt="rstudio default session" style="width: 1000px;" class="figure mx-auto d-block"></figure><ul><li>
 <strong>Source</strong>: This pane is where you will write/view R
@@ -633,8 +620,7 @@ <h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label=
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-uploads-and-downloads-in-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: Uploads and downloads in the cloud</h3>
 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
 cloud instance (click the “more” button) to your local computer. Uploads
@@ -653,8 +639,7 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="you-are-working-with-r" class="callout-inner">
-<h3 class="callout-title">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a>
-</h3>
+<h3 class="callout-title">You are working with R</h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
 of reasons to. For example, once you have written an RScript, you can
@@ -665,8 +650,7 @@ <h3 class="callout-title">You are working with R<a class="anchor" aria-label="an
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
-<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a></h2>
+</section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a></h2>
 <hr class="half-width"><p>Now that we have covered the more aesthetic aspects of RStudio, we
 can get to work using some commands. We will write, execute, and save
 the commands we learn in our <strong>genomics_r_basics.R</strong> script
@@ -708,8 +692,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-work-interactively-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" aria-label="anchor" href="#exercise-work-interactively-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Work interactively in R</h3>
 <div class="callout-content">
 <p>What happens when you try to enter the <code>getwd()</code> command
 in the Console pane?</p>
@@ -768,7 +751,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-never-use-setwd" class="callout-inner">
-<h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
+<h3 class="callout-title">Tip: Never use <code>setwd()</code>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -785,8 +768,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
-<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a></h2>
+</section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a></h2>
 <hr class="half-width"><p>A function in R (or any computing language) is a short program that
 takes some input and returns some output. Functions may seem like an
 advanced topic (and they are), but you have already used at least one
@@ -797,8 +779,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-what-do-these-functions-do" class="callout-inner">
-<h3 class="callout-title">Exercise: What do these functions do?<a class="anchor" aria-label="anchor" href="#exercise-what-do-these-functions-do"></a>
-</h3>
+<h3 class="callout-title">Exercise: What do these functions do?</h3>
 <div class="callout-content">
 <p>Try the following functions by writing them in your script. See if
 you can guess what they do, and make sure to add comments to your script
@@ -853,8 +834,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 3</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a></h2>
+</section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a></h2>
 <hr class="half-width"><p>What if you wanted to round to one significant digit?
 <code>round()</code> can do this, but you may first need to read the
 help to find out how. To see the help (In R sometimes also called a
@@ -943,8 +923,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-searching-for-r-functions" class="callout-inner">
-<h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" aria-label="anchor" href="#exercise-searching-for-r-functions"></a>
-</h3>
+<h3 class="callout-title">Exercise: Searching for R functions</h3>
 <div class="callout-content">
 <p>Use <code>help.search()</code> to find R functions for the following
 statistical functions. Remember to put your search query in quotes
@@ -981,8 +960,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 important ones are <a href="https://cran.r-project.org/" class="external-link">CRAN</a> - the
 main repository for R, and <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> - a popular repository
 for bioinformatics-related R packages.</p>
-</section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
-<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a></h2>
+</section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a></h2>
 <hr class="half-width"><p>Here is one last bonus we will mention about RStudio. It’s difficult
 to remember all of the arguments and definitions associated with a given
 function. When you start typing the name of a function and hit the
@@ -996,8 +974,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>R is a powerful, popular open-source scripting language</li>
 <li>You can customize the layout of RStudio, and use the project feature
@@ -1043,7 +1020,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1066,7 +1043,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/00-introduction.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/01-r-basics.html b/01-r-basics.html
index f7f102db..bff537c7 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
@@ -302,10 +302,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -325,7 +325,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -398,8 +398,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r">“The fantastic world of R awaits you” OR “Nobody wants to learn how
-to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
-<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a></h2>
+to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a></h2>
 <hr class="half-width"><p>Before we begin this lesson, we want you to be clear on the goal of
 the workshop and these lessons. We believe that every learner can
 <strong>achieve competency with R</strong>. You have reached competency
@@ -412,8 +411,7 @@ <h3 class="card-title">Objectives</h3>
 get, the more complex the analyses you will be able to carry out, with
 less frustration, and in less time - the fantastic world of R awaits
 you!</p>
-</section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
-<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a></h2>
+</section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a></h2>
 <hr class="half-width"><p>Nobody wants to learn how to use R. People want to learn how to use R
 to analyze their own research questions! Ok, maybe some folks learn R
 for R’s sake, but these lessons assume that you want to start analyzing
@@ -439,8 +437,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-where-to-learn-more" class="callout-inner">
-<h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
-</h3>
+<h3 class="callout-title">Tip: Where to learn more</h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
 them can be quite technical, but if you are a regular R user you may
@@ -470,15 +467,13 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a></h2>
+</section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a></h2>
 <hr class="half-width"><div id="reminder" class="callout prereq">
 <div class="callout-square">
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="reminder" class="callout-inner">
-<h3 class="callout-title">Reminder<a class="anchor" aria-label="anchor" href="#reminder"></a>
-</h3>
+<h3 class="callout-title">Reminder</h3>
 <div class="callout-content">
 <p>At this point you should be coding along in the
 “<strong>genomics_r_basics.R</strong>” script we created in the last
@@ -537,8 +532,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-some-objects-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" aria-label="anchor" href="#exercise-create-some-objects-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create some objects in R</h3>
 <div class="callout-content">
 <p>Create the following objects; give each object an appropriate name
 (your best guess at what name to use is fine):</p>
@@ -572,8 +566,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a></h2>
+</section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a></h2>
 <hr class="half-width"><p>Here are some important details about naming objects in R.</p>
 <ul><li>
 <strong>Avoid spaces and special characters</strong>: Object names
@@ -616,8 +609,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout-inner">
-<h3 class="callout-title">Tip: Pay attention to warnings in the script console<a class="anchor" aria-label="anchor" href="#tip-pay-attention-to-warnings-in-the-script-console"></a>
-</h3>
+<h3 class="callout-title">Tip: Pay attention to warnings in the script console</h3>
 <div class="callout-content">
 <p>If you enter a line of code in your script that contains an error,
 RStudio may give you an error message and underline this mistake.
@@ -630,8 +622,7 @@ <h3 class="callout-title">Tip: Pay attention to warnings in the script console<a
 <figure><img src="fig/rstudio_script_warning.png" alt="rstudio script warning" style="width: 600px;" class="figure mx-auto d-block"></figure></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
-<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a></h2>
+</section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a></h2>
 <hr class="half-width"><p>Once an object has a value, you can change that value by overwriting
 it. R will not give you a warning or error if you overwriting an object,
 which may or may not be a good thing depending on how you look at
@@ -661,8 +652,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
-<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a></h2>
+</section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a></h2>
 <hr class="half-width"><p>In R, <strong>every object has several properties</strong>:</p>
 <ul><li>
 <strong>Length</strong>: How many distinct values are held in that
@@ -682,8 +672,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-classess-vs.-modes" class="callout-inner">
-<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
-</h3>
+<h3 class="callout-title">Tip: Classess vs. modes</h3>
 <div class="callout-content">
 <p>The difference between modes and classes is a bit
 <strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
@@ -732,8 +721,7 @@ <h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-modes" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their modes<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-modes"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their modes</h3>
 <div class="callout-content">
 <p>Create the following objects in R, then use the <code>mode()</code>
 function to verify their modes. Try to guess what the mode will be
@@ -817,8 +805,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their class using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their class using “class”</h3>
 <div class="callout-content">
 <p>Using the objects created in the previous challenge, use the
 <code>class()</code> function to check their classes.</p>
@@ -928,8 +915,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
-<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a></h2>
+</section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a></h2>
 <hr class="half-width"><p>Once an object exists (which by definition also means it has a mode),
 R can appropriately manipulate that object. For example, objects of the
 numeric modes can be added, multiplied, divided, etc. R provides several
@@ -982,8 +968,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-compute-the-golden-ratio" class="callout-inner">
-<h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" aria-label="anchor" href="#exercise-compute-the-golden-ratio"></a>
-</h3>
+<h3 class="callout-title">Exercise: Compute the golden ratio</h3>
 <div class="callout-content">
 <p>One approximation of the golden ratio (φ) can be found by taking the
 sum of 1 and the square root of 5, and dividing by 2 as in the example
@@ -1016,8 +1001,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a>
-<a class="anchor" aria-label="anchor" href="#vectors"></a></h2>
+</section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a></h2>
 <hr class="half-width"><p>Vectors are probably the most used commonly used object type in R.
 <strong>A vector is a collection of values that are all of the same type
 (numbers, characters, etc.)</strong>. One of the most common ways to
@@ -1076,8 +1060,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 with later in this lesson, data frames, are collections of vectors. What
 we learn here about vectors will pay off even more when we start working
 with data frames.</p>
-</section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a></h2>
+</section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a></h2>
 <hr class="half-width"><p>Let’s create a few more vectors to play around with:</p>
 <div class="codewrapper sourceCode" id="cb44">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1156,8 +1139,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a></h2>
+</section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a></h2>
 <hr class="half-width"><p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
@@ -1227,8 +1209,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-examining-and-subsetting-vectors" class="callout-inner">
-<h3 class="callout-title">Exercise: Examining and subsetting vectors<a class="anchor" aria-label="anchor" href="#exercise-examining-and-subsetting-vectors"></a>
-</h3>
+<h3 class="callout-title">Exercise: Examining and subsetting vectors</h3>
 <div class="callout-content">
 <p>Answer the following questions to test your knowledge of vectors</p>
 <p>Which of the following are true of vectors in R? A) All vectors have
@@ -1262,8 +1243,7 @@ <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
-<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a></h2>
+</section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a></h2>
 <hr class="half-width"><p>There is one last set of cool subsetting capabilities we want to
 introduce. It is possible within R to retrieve items in a vector based
 on a logical evaluation or numerical comparison. For example, let’s say
@@ -1309,8 +1289,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-magic-of-programming" class="callout-inner">
-<h3 class="callout-title">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
-</h3>
+<h3 class="callout-title">The magic of programming</h3>
 <div class="callout-content">
 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
@@ -1387,8 +1366,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
-<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a></h2>
+</section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a></h2>
 <hr class="half-width"><p>Finally, there are a few other common retrieve or replace operations
 you may want to know about. First, you can check to see if any of the
 values of your vector are missing (i.e. are <code>NA</code>, that stands
@@ -1436,8 +1414,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="tip-whats-the-difference-between-the-in-and-the-operators" class="callout-inner">
 <h3 class="callout-title">Tip: What’s the difference between the
-<code>%in% and the</code>==` operators?<a class="anchor" aria-label="anchor" href="#tip-whats-the-difference-between-the-in-and-the-operators"></a>
-</h3>
+<code>%in% and the</code>==` operators?</h3>
 <div class="callout-content">
 <p>The <code>%in%</code> operator is used to test if the elements of a
 vector are present in another vector. In the example above, if both
@@ -1464,8 +1441,7 @@ <h3 class="callout-title">Tip: What’s the difference between the
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-1" class="callout-inner">
-<h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor" href="#review-exercise-1"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 1</h3>
 <div class="callout-content">
 <p>What data modes are the following vectors? a. <code>snps</code><br>
 b. <code>snp_chromosomes</code><br>
@@ -1522,8 +1498,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-2" class="callout-inner">
-<h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor" href="#review-exercise-2"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 2</h3>
 <div class="callout-content">
 <p>Add the following values to the specified vectors: a. To the
 <code>snps</code> vector add: “rs662799”<br>
@@ -1584,8 +1559,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-3" class="callout-inner">
-<h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor" href="#review-exercise-3"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 3</h3>
 <div class="callout-content">
 <p>Make the following change to the <code>snp_genes</code> vector:</p>
 <p>Hint: Your vector should look like this in ‘Environment’:
@@ -1628,8 +1602,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-4" class="callout-inner">
-<h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor" href="#review-exercise-4"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 4</h3>
 <div class="callout-content">
 <p>Using indexing, create a new vector named <code>combined</code> that
 contains:</p>
@@ -1672,8 +1645,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-5" class="callout-inner">
-<h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor" href="#review-exercise-5"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 5</h3>
 <div class="callout-content">
 <p>What type of data is <code>combined</code>?</p>
 </div>
@@ -1706,8 +1678,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="lists" class="callout-inner">
-<h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
-</h3>
+<h3 class="callout-title">Lists</h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
 genomics lessons. That said, you may come across lists in the way that
@@ -1782,8 +1753,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Effectively using R is a journey of months or years. Still you don’t
 have to be an expert to use R and you can start using and analyzing your
@@ -1832,7 +1802,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 	<div id="to-top">
@@ -1855,7 +1825,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
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               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
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                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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@@ -317,7 +317,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -383,8 +383,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a>
-<a class="anchor" aria-label="anchor" href="#preface"></a></h2>
+<section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a></h2>
 <hr class="half-width"><p>The Intro to R and RStudio for Genomics is a part of the Genomics
 Data Carpentry lessons. In this lesson we will learn the necessary skill
 sets for R and RStudio and apply them directly to a real next-generation
@@ -400,8 +399,7 @@ <h3 class="card-title">Objectives</h3>
 to characterize changes in sequence <em>a priori</em>
 </li>
 <li>Dataset publicly available - in this case through the NCBI SRA (<a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">http://www.ncbi.nlm.nih.gov/sra</a>)</li>
-</ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a></h2>
+</ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a></h2>
 <hr class="half-width"><p>Microbes are ideal organisms for exploring ‘Long-term Evolution
 Experiments’ (LTEEs) - thousands of generations can be generated and
 stored in a way that would be virtually impossible for more complex
@@ -461,8 +459,7 @@ <h3 class="card-title">Objectives</h3>
 <ul><li>How many base pair changes are there between the Cit+ and Cit-
 strains?</li>
 <li>What are the base pair changes between strains?</li>
-</ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
-<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a></h2>
+</ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a></h2>
 <hr class="half-width"><p>Publicly accessible sequencing files in FASTQ formats can be
 downloaded from NCBI SRA. However, at FASTQ files contain unaligned
 sequences of varying quality, and requires clean up and alignment steps
@@ -472,8 +469,7 @@ <h3 class="card-title">Objectives</h3>
 bioinformatics tools that are used:</p>
 <center>
 <img src="fig/variant_calling_workflow.png" alt="variant calling workflow. Sequence reads (FASTQ files), Quality control (FASTQ files), Alignment to Genome (SAM/BAM files), Alignment cleanup (BAM file ready for variant calling), Variant Calling (VCF file)" style="width: 250px;" class="figure"></center>
-</section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
-<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a></h2>
+</section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a></h2>
 <hr class="half-width"><p>VCF files contain variants that were called against a reference
 genome. These files are slightly more complicated than regular tables
 you can open using programs like Excel and contain two sections: header
@@ -571,8 +567,7 @@ <h3 class="card-title">Objectives</h3>
 <td>the Phred-scaled confidence for the genotype</td>
 </tr></tbody></table><p>For more information on VCF files visit The Broad Institute’s <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" class="external-link">VCF
 guide</a>.</p>
-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -590,8 +585,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The dataset comes from a real world experiment in E. coli.</li>
 <li>Publicly available FASTQ files can be downloaded from NCBI SRA.</li>
@@ -637,7 +631,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -660,7 +654,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/02-data-prelude.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index e19ad00a..5d716a47 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -301,10 +301,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -324,7 +324,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -406,8 +406,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
-<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a></h2>
+<section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a></h2>
 <hr class="half-width"><p>A substantial amount of the data we work with in genomics will be
 tabular data, this is data arranged in rows and columns - also known as
 spreadsheets. We could write a whole lesson on how to work with
@@ -443,8 +442,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-keep-your-raw-data-separate" class="callout-inner">
-<h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
-</h3>
+<h3 class="callout-title">Tip: Keep your raw data separate</h3>
 <div class="callout-content">
 <p>When you work with data in R, you are not changing the original file
 you loaded that data from. This is different than (for example) working
@@ -456,8 +454,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
-<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a></h2>
+</section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a></h2>
 <hr class="half-width"><p>There are several ways to import data into R. For our purpose here,
 we will focus on using the tools every R installation comes with (so
 called “base” R) to import a comma-delimited file containing the results
@@ -469,8 +466,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 <div id="exercise-review-the-arguments-of-the-read.csv-function" class="callout-inner">
 <h3 class="callout-title">Exercise: Review the arguments of the
-<code>read.csv()</code> function<a class="anchor" aria-label="anchor" href="#exercise-review-the-arguments-of-the-read.csv-function"></a>
-</h3>
+<code>read.csv()</code> function</h3>
 <div class="callout-content">
 <p><strong>Before using the <code>read.csv()</code> function, use R’s
 help feature to answer the following questions</strong>.</p>
@@ -495,7 +491,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
@@ -522,8 +518,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
-<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
-</h3>
+<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?</h3>
 <div class="callout-content">
 <p>The reason for this is because <code>read.csv</code> is actually a
 short cut for <code>read.table("file.csv", sep = ",")</code>. You can
@@ -563,8 +558,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 name of the object will open a view of the data in a new tab.</p>
 <figure><img src="%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure></section><section><h2 class="section-heading" id="summarizing-subsetting-and-determining-the-structure-of-a-data-frame-">Summarizing, subsetting, and determining the structure of a data
-frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame."></a>
-<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a></h2>
+frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a></h2>
 <hr class="half-width"><p>A <strong>data frame is the standard way in R to store tabular
 data</strong>. A data fame could also be thought of as a collection of
 vectors, all of which have the same length. Using only two functions, we
@@ -690,8 +684,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
-</h3>
+<h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
 <div class="callout-content">
 <p>Remeber when we said mode and class are sometimes different? If you
 do, here is a chance to check. What happens when you try the
@@ -706,7 +699,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -742,8 +735,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </li>
-</ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-factors"></a></h2>
+</ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a></h2>
 <hr class="half-width"><p>Factors are the final major data structure we will introduce in our R
 genomics lessons. Factors can be thought of as vectors which are
 specialized for categorical data. Given R’s specialization for
@@ -875,8 +867,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
-<h3 class="callout-title">Tip: treating objects as categories without changing their mode<a class="anchor" aria-label="anchor" href="#tip-treating-objects-as-categories-without-changing-their-mode"></a>
-</h3>
+<h3 class="callout-title">Tip: treating objects as categories without changing their mode</h3>
 <div class="callout-content">
 <p>You don’t have to make an object a factor to get the benefits of
 treating an object as a factor. See what happens when you use the
@@ -887,8 +878,7 @@ <h3 class="callout-title">Tip: treating objects as categories without changing t
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
-<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a></h2>
+</section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a></h2>
 <hr class="half-width"><p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
@@ -943,8 +933,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout-inner">
-<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?<a class="anchor" aria-label="anchor" href="#tip-packages-in-r-what-are-they-and-why-do-we-use-them"></a>
-</h3>
+<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?</h3>
 <div class="callout-content">
 <p>Packages are simply collections of functions and/or data that can be
 used to extend the capabilities of R beyond the core functionality that
@@ -978,8 +967,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a></h2>
+</section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a></h2>
 <hr class="half-width"><p>Next, we are going to talk about how you can get specific values from
 data frames, and where necessary, change the mode of a column of
 values.</p>
@@ -993,8 +981,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-subsetting-a-data-frame" class="callout-inner">
-<h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" aria-label="anchor" href="#exercise-subsetting-a-data-frame"></a>
-</h3>
+<h3 class="callout-title">Exercise: Subsetting a data frame</h3>
 <div class="callout-content">
 <p><strong>Try the following indices and functions and try to figure out
 what they return</strong></p>
@@ -1018,7 +1005,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol><div class="codewrapper sourceCode" id="cb30">
@@ -1413,15 +1400,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
                                        Max.   :1
                                                                      </code></pre>
 </div>
-</section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a></h2>
+</section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a></h2>
 <hr class="half-width"><div id="tip-coercion-isnt-limited-to-data-frames" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>While we are going to address coercion in the context of data frames
 most of these methods apply to other data structures, such as
@@ -1615,8 +1600,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
-<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a></h2>
+</section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a></h2>
 <hr class="half-width"><p>Lets summarize this section on coercion with a few take home
 messages.</p>
 <ul><li>When you explicitly coerce one data type into another (this is known
@@ -1634,8 +1618,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames-1"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>Prior to R 4.0 when importing a data frame using any one of the
 <code>read.table()</code> functions such as <code>read.csv()</code> ,
@@ -1649,8 +1632,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
-<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a></h2>
+</section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a></h2>
 <hr class="half-width"><p>Here are a few operations that don’t need much explanation, but which
 are good to know.</p>
 <p>There are lots of arithmetic functions you may want to apply to your
@@ -1694,8 +1676,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>The <code>order()</code> function lists values in increasing order by
 default. Look at the documentation for this function and change
@@ -1709,7 +1690,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1749,8 +1730,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [25] "MQ"            "Indiv"         "gt_PL"         "gt_GT"
 [29] "gt_GT_alleles"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
-<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a></h2>
+</section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a></h2>
 <hr class="half-width"><p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
@@ -1765,8 +1745,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to write to file, and give a path to a file name in quotes (if you only
 provide a file name, the file will be written in the current working
 directory).</p>
-</section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
-<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a></h2>
+</section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a></h2>
 <hr class="half-width"><p>Excel is one of the most common formats, so we need to discuss how to
 make these files play nicely with R. The simplest way to import data
 from Excel is to <strong>save your Excel file in .csv format</strong>*.
@@ -1829,8 +1808,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-putting-it-all-together---data-frames" class="callout-inner">
-<h3 class="callout-title">Exercise: Putting it all together - data frames<a class="anchor" aria-label="anchor" href="#exercise-putting-it-all-together---data-frames"></a>
-</h3>
+<h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <div class="callout-content">
 <p><strong>Using the <code>Ecoli_metadata</code> data frame created
 above, answer the following questions</strong></p>
@@ -1858,7 +1836,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data frames<a clas
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-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
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 <div class="codewrapper sourceCode" id="cb91">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>It is easy to import data into R from tabular formats including
 Excel. However, you still need to check that R has imported and
@@ -1987,7 +1964,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 	<div id="to-top">
@@ -2010,7 +1987,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/04-bioconductor-vcfr.html b/04-bioconductor-vcfr.html
index e22dff7a..8c3d86db 100644
--- a/04-bioconductor-vcfr.html
+++ b/04-bioconductor-vcfr.html
@@ -296,10 +296,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -387,8 +387,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
-<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a></h2>
+<section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a></h2>
 <hr class="half-width"><p>So far we have told you about using packages that are included in the
 base installation of R (this is what comes with R ‘out of the box’), and
 packages that you can install from <a href="https://cran.r-project.org/" class="external-link">CRAN</a> (the Comprehensive R Archive
@@ -403,16 +402,14 @@ <h3 class="card-title">Objectives</h3>
 all of the packages available on Bioconductor are focused on the
 analysis of biological data, and that it can be a great place to look
 for tools to help you analyze your -omics datasets!</p>
-</section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
-<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a></h2>
+</section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a></h2>
 <hr class="half-width"><p>Since access to the <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> repository is not
 built in to base R ‘out of the box’, there are a couple steps needed to
 install packages from this alternative source. We will work through the
 steps (only 2!) to install a package to help with the VCF analysis we
 are working on, but you can use the same approach to install any of the
 many thousands of available packages.</p>
-<figure><img src="fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
-<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a></h2>
+<figure><img src="fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a></h2>
 <hr class="half-width"><p>The first step is to install a package that <em>is</em> on CRAN,
 <code>BiocManager</code>. This package will allow us to use it to
 install packages from Bioconductor. You can think of Bioconductor kind
@@ -438,15 +435,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">version</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager">Second, install the vcfR package from Bioconductor using
-<code>BiocManager</code><a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a>
+<code>BiocManager</code>
 <a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a></h2>
 <hr class="half-width"><div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout">
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-</h3>
+<h3 class="callout-title">Head’s Up: Installing vcfR may take a while due to numerous dependencies</h3>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
 can take a while.</p>
@@ -468,8 +464,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
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-</h3>
+<h3 class="callout-title">Note: Installing packages from Bioconductor vs from CRAN</h3>
 <div class="callout-content">
 <p>Some packages begin by being available only on Bioconductor, and then
 later move to CRAN. <code>vcfR</code> is one such package, which
@@ -487,8 +482,7 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
-<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a></h2>
+</section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a></h2>
 <hr class="half-width"><p>While we are only focusing in this workshop on VCF analyses, there
 are hundreds or thousands of different types of data and analyses that
 bioinformaticians may want to work with. Sometimes you may get a new
@@ -500,8 +494,7 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout-inner">
-<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website<a class="anchor" aria-label="anchor" href="#tip-searching-for-packages-on-the-bioconductor-website"></a>
-</h3>
+<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website</h3>
 <div class="callout-content">
 <p>There are several thousand packages available through the
 Bioconductor website. It can be a bit of a challenge to find what you
@@ -520,8 +513,7 @@ <h3 class="callout-title">Tip: Searching for packages on the Bioconductor websit
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul><li>Use the <code>BiocManager::available()</code> function to see what
 packages are available matching a search term.</li>
@@ -538,8 +530,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-refreshing-the-rstudio-package-view-after-installing" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Tip: Refreshing the RStudio package view after installing</h3>
 <div class="callout-content">
 <p>If you install a package from Bioconductor, you may need to refresh
 the RStudio package view to see it in your list. You can do this by
@@ -547,8 +538,7 @@ <h3 class="callout-title">Tip: Refreshing the RStudio package view after install
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
+</section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
 <hr class="half-width"><ul><li><a href="https://bioconductor.org/" class="external-link">Bioconductor</a></li>
 <li><a href="https://bioconductor.org/packages/release/BiocViews.html#___Software" class="external-link">Bioconductor
 package search</a></li>
@@ -558,8 +548,7 @@ <h3 class="callout-title">Tip: Refreshing the RStudio package view after install
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Bioconductor is an alternative package repository for bioinformatics
 packages.</li>
@@ -607,7 +596,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -630,7 +619,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/04-bioconductor-vcfr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/05-dplyr.html b/05-dplyr.html
index 44839f45..e7f61ce2 100644
--- a/05-dplyr.html
+++ b/05-dplyr.html
@@ -290,10 +290,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -313,7 +313,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -437,8 +437,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="tip-installing-packages" class="callout-inner">
-<h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
-</h3>
+<h3 class="callout-title">Tip: Installing packages</h3>
 <div class="callout-content">
 <p>It may be temping to install the <code>tidyverse</code> package, as
 it contains many useful collection of packages for this lesson and
@@ -450,8 +449,7 @@ <h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
-<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a></h2>
+<section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a></h2>
 <hr class="half-width"><p>The package <code>dplyr</code> is a fairly new (2014) package that
 tries to provide easy tools for the most common data manipulation tasks.
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@@ -623,8 +621,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Create a table that contains all the columns with the letter “i” and
 column “POS”, without columns “Indiv” and “FILTER”. Hint: look at for a
@@ -678,7 +675,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<em> (continued)</em><a class="anchor" aria-label="anchor" href="#challenge"></a>
+<h3 class="callout-title">Challenge<em> (continued)</em>
 </h3>
 <div class="callout-content">
 <p>We can also get to <code>variants_result</code> in one line of
@@ -946,8 +943,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Select all the mutations that occurred between the positions 1e6 (one
 million) and 2e6 (inclusive) that have a QUAL greater than 200, and
@@ -1145,8 +1141,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-pipe-and-filter" class="callout-inner">
-<h3 class="callout-title">Exercise: Pipe and filter<a class="anchor" aria-label="anchor" href="#exercise-pipe-and-filter"></a>
-</h3>
+<h3 class="callout-title">Exercise: Pipe and filter</h3>
 <div class="callout-content">
 <p>Starting with the <code>variants</code> data frame, use pipes to
 subset the data to include only observations from SRR2584863 sample,
@@ -1237,8 +1232,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>There are a lot of columns in our data set, so let’s just look at the
 <code>sample_id</code>, <code>POS</code>, <code>QUAL</code>, and
@@ -1337,8 +1331,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul><li>How many mutations are INDELs?</li>
 </ul></div>
@@ -1421,8 +1414,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="grouped-data-frames-in-tidyverse" class="callout-inner">
-<h3 class="callout-title">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a>
-</h3>
+<h3 class="callout-title">Grouped Data Frames in Tidyverse</h3>
 <div class="callout-content">
 <p>When you group a data frame with <code>group_by()</code>, you get a
 grouped data frame. This is a special type of data frame that has all
@@ -1514,8 +1506,7 @@ <h3 id="resources">Resources<a class="anchor" aria-label="anchor" href="#resourc
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Use the <code>dplyr</code> package to manipulate data frames.</li>
 <li>Use <code>glimpse()</code> to quickly look at your data frame.</li>
@@ -1573,7 +1564,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1596,7 +1587,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/05-dplyr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/06-data-visualization.html b/06-data-visualization.html
index d81bf954..a6b78c53 100644
--- a/06-data-visualization.html
+++ b/06-data-visualization.html
@@ -299,10 +299,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -322,7 +322,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -400,7 +400,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong><a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
+<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong>
 <a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a></h2>
 <hr class="half-width"><figure><img src="https://ggplot2.tidyverse.org/logo.png" align="right" alt="Line plot enclosed in hexagon shape with ggplot2 typed beneath and www.rstudio.com at the bottom." class="figure mx-auto d-block"></figure><p><strong><code>ggplot2</code></strong> is a plotting package, part of
 the tidyverse, that makes it simple to create complex plots from data in
@@ -438,7 +438,7 @@ <h3 class="card-title">Objectives</h3>
 or discrete</a>, a quick way to check is to use the <a href="https://www.geeksforgeeks.org/get-summary-of-results-produced-by-functions-in-r-programming-summary-function/" class="external-link"><code>summary()</code></a>
 function. Continuous variables have descriptive statistics but not the
 discrete variables.</p>
-</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code><a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
+</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code>
 <a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a></h2>
 <hr class="half-width"><p>First, we need to install the <code>ggplot2</code> package.</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -486,8 +486,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>As we can see from above output <strong><code>ggplot2</code></strong>
 has been already loaded along with other packages as part of the
 <strong><code>tidyverse</code></strong> framework.</p>
-</section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a></h2>
+</section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a></h2>
 <hr class="half-width"><div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
@@ -848,8 +847,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">coverage_plot</span></span>
 <span>  <span class="op">+</span> <span class="fu">geom_point</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
-<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a></h2>
+</section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a></h2>
 <hr class="half-width"><p>Building plots with <strong><code>ggplot2</code></strong> is
 typically an iterative process. We start by defining the dataset we’ll
 use, lay out the axes, and choose a geom:</p>
@@ -941,8 +939,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of mapping quality
 (<code>MQ</code>) over position (<code>POS</code>) with the samples
@@ -956,7 +953,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -984,8 +981,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>       title <span class="op">=</span> <span class="st">"Read Depth vs. Position"</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">theme</span><span class="op">(</span>text <span class="op">=</span> <span class="fu">element_text</span><span class="op">(</span>family <span class="op">=</span> <span class="st">"Bookman"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a>
-<a class="anchor" aria-label="anchor" href="#faceting"></a></h2>
+<figure><img src="fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a></h2>
 <hr class="half-width"><p><strong><code>ggplot2</code></strong> has a special technique called
 <em>faceting</em> that allows the user to split one plot into multiple
 plots (panels) based on a factor (variable) included in the dataset. We
@@ -1038,8 +1034,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of PHRED scaled
 quality (<code>QUAL</code>) over position (<code>POS</code>) with the
@@ -1053,7 +1048,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1069,8 +1064,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a>
-<a class="anchor" aria-label="anchor" href="#barplots"></a></h2>
+</section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a></h2>
 <hr class="half-width"><p>We can create barplots using the <a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link"><code>geom_bar</code></a>
 geom. Let’s make a barplot showing the number of variants for each
 sample that are indels.</p>
@@ -1087,8 +1081,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Since we already have the sample_id labels on the individual plot
 facets, we don’t need the legend. Use the help file for
@@ -1102,7 +1095,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1116,8 +1109,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a>
-<a class="anchor" aria-label="anchor" href="#density"></a></h2>
+</section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a></h2>
 <hr class="half-width"><p>We can create density plots using the <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 geom that shows the distribution of of a variable in the dataset. Let’s
 plot the distribution of <code>DP</code></p>
@@ -1135,8 +1127,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-3" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-3"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 to plot the distribution of <code>DP</code> with a different fill for
@@ -1149,7 +1140,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1164,8 +1155,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="ggplot2-themes">
-<strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
-<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a></h2>
+<strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a></h2>
 <hr class="half-width"><p>In addition to <a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link"><code>theme_bw()</code></a>,
 which changes the plot background to white,
 <strong><code>ggplot2</code></strong> comes with several other themes
@@ -1187,8 +1177,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="challenge-4" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-4"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>With all of this information in hand, please take another five
 minutes to either improve one of the plots generated in this exercise or
@@ -1202,8 +1191,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
-<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a></h2>
+</section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a></h2>
 <hr class="half-width"><p><strong><code>ggplot2</code></strong> offers many more informative
 and beautiful plots (<code>geoms</code>) of interest for biologists
 (although not covered in this lesson) that are worth exploring, such
@@ -1217,8 +1205,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <li>
 <a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link"><code>geom_violin()</code></a>,
 for violin plots</li>
-</ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
+</ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
 <hr class="half-width"><ul><li>
 <a href="https://www.amazon.com/gp/product/331924275X/" class="external-link">ggplot2:
 Elegant Graphics for Data Analysis</a> (<a href="https://ggplot2-book.org/" class="external-link">online version</a>)</li>
@@ -1235,8 +1222,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>ggplot2 is a powerful tool for high-quality plots</li>
 <li>ggplot2 provides a flexible and readable grammar to build plots</li>
@@ -1279,7 +1265,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1302,7 +1288,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/06-data-visualization.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
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diff --git a/07-r-help.html b/07-r-help.html
index 753652f2..be537cfc 100644
--- a/07-r-help.html
+++ b/07-r-help.html
@@ -293,10 +293,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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                 </h2>
@@ -316,7 +316,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -385,8 +385,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a></h2>
+<section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a></h2>
 <hr class="half-width"><figure><img src="fig/oreilly_book_covers.png" alt="rstudio default session" style="width: 600px;" class="figure mx-auto d-block"></figure><p>No matter how much experience you have with R, you will find yourself
 needing help. There is no shame in researching how to do something in R,
 and most people will find themselves looking up how to do the same
@@ -395,8 +394,7 @@ <h3 class="card-title">Objectives</h3>
 <blockquote>
 <p>“Never memorize something that you can look up” -- A. Einstein</p>
 </blockquote>
-</section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
-<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a></h2>
+</section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a></h2>
 <hr class="half-width"><p>Two popular websites will be of great help with many R problems. For
 <strong>general</strong> <strong>R questions</strong>, <a href="https://stackoverflow.com/" class="external-link">Stack Overflow</a> is probably the
 most popular online community for developers. If you start your question
@@ -408,8 +406,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-asking-for-help-using-online-forums" class="callout-inner">
-<h3 class="callout-title">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
-</h3>
+<h3 class="callout-title">Tip: Asking for help using online forums:</h3>
 <div class="callout-content">
 <ul><li>When searching for R help, look for <a href="https://stackoverflow.com/questions/tagged/r" class="external-link">answers with the ‘r’
 tag</a>.</li>
@@ -425,8 +422,7 @@ <h3 class="callout-title">Tip: Asking for help using online forums:<a class="anc
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
-<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a></h2>
+</section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a></h2>
 <hr class="half-width"><p>Often, in order to duplicate the issue you are having, someone may
 need to see the data you are working with or verify the versions of R or
 R packages you are using. The following R functions will help with
@@ -485,8 +481,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">saveRDS</span><span class="op">(</span><span class="va">iris</span>, file<span class="op">=</span><span class="st">"iris.rds"</span><span class="op">)</span> <span class="co"># By convention, we use the .rds file extension</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
-<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a></h2>
+</section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a></h2>
 <hr class="half-width"><p>Finally, here are a few pieces of introductory R knowledge that are
 too good to pass up. While we won’t return to them in this course, we
 put them here because they come up commonly:</p>
@@ -537,8 +532,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>R provides thousands of functions for analyzing data, and provides
 several way to get help</li>
@@ -583,7 +577,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -606,7 +600,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/07-r-help.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index d5ffa102..9a4d7e4b 100644
--- a/404.html
+++ b/404.html
@@ -298,10 +298,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -322,7 +322,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="https://datacarpentry.github.io/genomics-r-intro/aio.html" class="external-link">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="https://datacarpentry.github.io/genomics-r-intro/aio.html" class="external-link">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -339,8 +339,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Page not found</h1>
         
-<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
 <hr class="half-width"><p>We cannot seem to find the page you are looking for. Here are some
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 <ol style="list-style-type: decimal"><li>try going back to the <a href="javascript:history.back()">previous
@@ -375,7 +374,7 @@ <h1>Page not found</h1>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -397,8 +396,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/404.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
-  "datePublished": "2024-08-20"
+  "dateModified": "2024-08-27",
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 1025c916..0e62a849 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -302,7 +302,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -390,7 +390,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -413,7 +413,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/CODE_OF_CONDUCT.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 1042aaad..b7089069 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -302,7 +302,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -345,8 +345,7 @@ <h1>Licenses</h1>
 
         
 
-<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
 Carpentry) instructional material is made available under the <a href="https://creativecommons.org/licenses/by/4.0/" class="external-link">Creative Commons
 Attribution license</a>. The following is a human-readable summary of
@@ -379,8 +378,7 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-<a class="anchor" aria-label="anchor" href="#software"></a></h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -400,8 +398,7 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
-</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
-<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -441,7 +438,7 @@ <h1>Licenses</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -464,7 +461,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/LICENSE.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 4d2d4888..6c874522 100644
--- a/aio.html
+++ b/aio.html
@@ -342,10 +342,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
             </div>
 
             <hr class="half-width">
-<div class="accordion accordion-flush resources" id="accordionFlush12">
+<div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources">
+            <hr class="half-width lesson-resources">
 <a href="aio.html">See all in one page</a>
 
 
@@ -439,7 +439,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
-<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
 </h2>
 <hr class="half-width">
 <p>In this lesson we will take you through the very first things you
@@ -449,8 +448,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anchor" aria-label="anchor" href="#tip-this-lesson-works-best-on-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: This lesson works best on the cloud</h3>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
 virtual machine instances provided to you at a genomics workshop. Much
@@ -463,7 +461,6 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 </div>
 </div>
 </section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
-<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
 </h2>
 <hr class="half-width">
 <p><a href="https://en.wikipedia.org/wiki/R_(programming_language)" class="external-link">The
@@ -473,7 +470,6 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 Labs and was developed to teach intro statistics. See this <a href="https://www.stat.auckland.ac.nz/~ihaka/downloads/Massey.pdf" class="external-link">slide
 deck</a> by Ross Ihaka for more info on the subject.</p>
 </section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
-<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
 </h2>
 <hr class="half-width">
 <p>At more than 20 years old, R is fairly mature and <a href="https://www.tiobe.com/tiobe-index/r/" class="external-link">growing in popularity</a>.
@@ -507,8 +503,7 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="discussion-your-experience" class="callout-inner">
-<h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-label="anchor" href="#discussion-your-experience"></a>
-</h3>
+<h3 class="callout-title">Discussion: Your experience</h3>
 <div class="callout-content">
 <p>What has motivated you to learn R? Have you had a research question
 for which spreadsheet programs such as Excel have proven difficult to
@@ -517,7 +512,6 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 </div>
 </div>
 </section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
 </h2>
 <hr class="half-width">
 <p>In these lessons, we will be making use of a software called <a href="https://www.rstudio.com/products/RStudio/" class="external-link">RStudio</a>, an <a href="https://en.wikipedia.org/wiki/Integrated_development_environment" class="external-link">Integrated
@@ -530,7 +524,6 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 browser. RStudio Server has the same features of the Desktop version of
 RStudio you could download as standalone software.</p>
 </section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
 </h2>
 <hr class="half-width">
 <p>Open a web browser and enter the URL you used to log in at the
@@ -543,8 +536,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout-inner">
-<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.<a class="anchor" aria-label="anchor" href="#tip-make-sure-there-are-no-spaces-before-or-after-your-url."></a>
-</h3>
+<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.</h3>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -558,7 +550,6 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 by your instructors.</p>
 <p>You should now see the RStudio interface:</p>
 <figure><img src="fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
-<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
 </h2>
 <hr class="half-width">
 <p>One of the first benefits we will take advantage of in RStudio is
@@ -606,8 +597,7 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-your-project-more-reproducible-with-renv" class="callout-inner">
-<h3 class="callout-title">Tip: Make your project more reproducible with renv<a class="anchor" aria-label="anchor" href="#tip-make-your-project-more-reproducible-with-renv"></a>
-</h3>
+<h3 class="callout-title">Tip: Make your project more reproducible with renv</h3>
 <div class="callout-content">
 <p>One of the most wonderful and also frustrating aspects of working
 with R is managing packages. We will talk more about them, but packages
@@ -626,7 +616,6 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 </div>
 </div>
 </section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a>
-<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a>
 </h2>
 <hr class="half-width">
 <p>Now that we are ready to start exploring R, we will want to keep a
@@ -646,8 +635,7 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-save-your-script-now" class="callout-inner">
-<h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label="anchor" href="#tip-save-your-script-now"></a>
-</h3>
+<h3 class="callout-title">Tip: Save your script now</h3>
 <div class="callout-content">
 <p>Remember to save your script at this point. Anything can happen
 during your lesson and you don’t want to lose your work!</p>
@@ -655,7 +643,6 @@ <h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label=
 </div>
 </div>
 </section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a>
-<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a>
 </h2>
 <hr class="half-width">
 <p>Here are the major windows (or panes) of the RStudio environment:</p>
@@ -696,8 +683,7 @@ <h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label=
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-uploads-and-downloads-in-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: Uploads and downloads in the cloud</h3>
 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
 cloud instance (click the “more” button) to your local computer. Uploads
@@ -716,8 +702,7 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="you-are-working-with-r" class="callout-inner">
-<h3 class="callout-title">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a>
-</h3>
+<h3 class="callout-title">You are working with R</h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
 of reasons to. For example, once you have written an RScript, you can
@@ -729,7 +714,6 @@ <h3 class="callout-title">You are working with R<a class="anchor" aria-label="an
 </div>
 </div>
 </section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
-<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
 </h2>
 <hr class="half-width">
 <p>Now that we have covered the more aesthetic aspects of RStudio, we
@@ -773,8 +757,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-work-interactively-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" aria-label="anchor" href="#exercise-work-interactively-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Work interactively in R</h3>
 <div class="callout-content">
 <p>What happens when you try to enter the <code>getwd()</code> command
 in the Console pane?</p>
@@ -833,7 +816,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-never-use-setwd" class="callout-inner">
-<h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
+<h3 class="callout-title">Tip: Never use <code>setwd()</code>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -851,7 +834,6 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 </div>
 </div>
 </section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
-<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
 </h2>
 <hr class="half-width">
 <p>A function in R (or any computing language) is a short program that
@@ -864,8 +846,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-what-do-these-functions-do" class="callout-inner">
-<h3 class="callout-title">Exercise: What do these functions do?<a class="anchor" aria-label="anchor" href="#exercise-what-do-these-functions-do"></a>
-</h3>
+<h3 class="callout-title">Exercise: What do these functions do?</h3>
 <div class="callout-content">
 <p>Try the following functions by writing them in your script. See if
 you can guess what they do, and make sure to add comments to your script
@@ -927,7 +908,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] 3</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
 </h2>
 <hr class="half-width">
 <p>What if you wanted to round to one significant digit?
@@ -1018,8 +998,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-searching-for-r-functions" class="callout-inner">
-<h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" aria-label="anchor" href="#exercise-searching-for-r-functions"></a>
-</h3>
+<h3 class="callout-title">Exercise: Searching for R functions</h3>
 <div class="callout-content">
 <p>Use <code>help.search()</code> to find R functions for the following
 statistical functions. Remember to put your search query in quotes
@@ -1061,7 +1040,6 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 main repository for R, and <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> - a popular repository
 for bioinformatics-related R packages.</p>
 </section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
-<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
 </h2>
 <hr class="half-width">
 <p>Here is one last bonus we will mention about RStudio. It’s difficult
@@ -1077,8 +1055,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>R is a powerful, popular open-source scripting language</li>
@@ -1133,7 +1110,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 <section><h2 class="section-heading" id="the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r">“The fantastic world of R awaits you” OR “Nobody wants to learn how
 to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
-<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
 </h2>
 <hr class="half-width">
 <p>Before we begin this lesson, we want you to be clear on the goal of
@@ -1149,7 +1125,6 @@ <h3 class="card-title">Objectives</h3>
 less frustration, and in less time - the fantastic world of R awaits
 you!</p>
 </section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
-<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
 </h2>
 <hr class="half-width">
 <p>Nobody wants to learn how to use R. People want to learn how to use R
@@ -1179,8 +1154,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-where-to-learn-more" class="callout-inner">
-<h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
-</h3>
+<h3 class="callout-title">Tip: Where to learn more</h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
 them can be quite technical, but if you are a regular R user you may
@@ -1213,7 +1187,6 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
 </h2>
 <hr class="half-width">
 <div id="reminder" class="callout prereq">
@@ -1221,8 +1194,7 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="reminder" class="callout-inner">
-<h3 class="callout-title">Reminder<a class="anchor" aria-label="anchor" href="#reminder"></a>
-</h3>
+<h3 class="callout-title">Reminder</h3>
 <div class="callout-content">
 <p>At this point you should be coding along in the
 “<strong>genomics_r_basics.R</strong>” script we created in the last
@@ -1295,8 +1267,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-some-objects-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" aria-label="anchor" href="#exercise-create-some-objects-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create some objects in R</h3>
 <div class="callout-content">
 <p>Create the following objects; give each object an appropriate name
 (your best guess at what name to use is fine):</p>
@@ -1333,7 +1304,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
 </h2>
 <hr class="half-width">
 <p>Here are some important details about naming objects in R.</p>
@@ -1382,8 +1352,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout-inner">
-<h3 class="callout-title">Tip: Pay attention to warnings in the script console<a class="anchor" aria-label="anchor" href="#tip-pay-attention-to-warnings-in-the-script-console"></a>
-</h3>
+<h3 class="callout-title">Tip: Pay attention to warnings in the script console</h3>
 <div class="callout-content">
 <p>If you enter a line of code in your script that contains an error,
 RStudio may give you an error message and underline this mistake.
@@ -1398,7 +1367,6 @@ <h3 class="callout-title">Tip: Pay attention to warnings in the script console<a
 </div>
 </div>
 </section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
-<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
 </h2>
 <hr class="half-width">
 <p>Once an object has a value, you can change that value by overwriting
@@ -1431,7 +1399,6 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
-<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
 <hr class="half-width">
 <p>In R, <strong>every object has several properties</strong>:</p>
@@ -1455,8 +1422,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-classess-vs.-modes" class="callout-inner">
-<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
-</h3>
+<h3 class="callout-title">Tip: Classess vs. modes</h3>
 <div class="callout-content">
 <p>The difference between modes and classes is a bit
 <strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
@@ -1521,8 +1487,7 @@ <h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-modes" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their modes<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-modes"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their modes</h3>
 <div class="callout-content">
 <p>Create the following objects in R, then use the <code>mode()</code>
 function to verify their modes. Try to guess what the mode will be
@@ -1608,8 +1573,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their class using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their class using “class”</h3>
 <div class="callout-content">
 <p>Using the objects created in the previous challenge, use the
 <code>class()</code> function to check their classes.</p>
@@ -1720,7 +1684,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
-<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width">
 <p>Once an object exists (which by definition also means it has a mode),
@@ -1799,8 +1762,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-compute-the-golden-ratio" class="callout-inner">
-<h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" aria-label="anchor" href="#exercise-compute-the-golden-ratio"></a>
-</h3>
+<h3 class="callout-title">Exercise: Compute the golden ratio</h3>
 <div class="callout-content">
 <p>One approximation of the golden ratio (φ) can be found by taking the
 sum of 1 and the square root of 5, and dividing by 2 as in the example
@@ -1834,7 +1796,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a>
-<a class="anchor" aria-label="anchor" href="#vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Vectors are probably the most used commonly used object type in R.
@@ -1896,7 +1857,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 we learn here about vectors will pay off even more when we start working
 with data frames.</p>
 </section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Let’s create a few more vectors to play around with:</p>
@@ -1978,7 +1938,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Once you have an existing vector, you may want to add a new item to
@@ -2050,8 +2009,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-examining-and-subsetting-vectors" class="callout-inner">
-<h3 class="callout-title">Exercise: Examining and subsetting vectors<a class="anchor" aria-label="anchor" href="#exercise-examining-and-subsetting-vectors"></a>
-</h3>
+<h3 class="callout-title">Exercise: Examining and subsetting vectors</h3>
 <div class="callout-content">
 <p>Answer the following questions to test your knowledge of vectors</p>
 <p>Which of the following are true of vectors in R? A) All vectors have
@@ -2092,7 +2050,6 @@ <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </div>
 </div>
 </section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
-<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
 </h2>
 <hr class="half-width">
 <p>There is one last set of cool subsetting capabilities we want to
@@ -2168,8 +2125,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-magic-of-programming" class="callout-inner">
-<h3 class="callout-title">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
-</h3>
+<h3 class="callout-title">The magic of programming</h3>
 <div class="callout-content">
 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
@@ -2247,7 +2203,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
-<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
 </h2>
 <hr class="half-width">
 <p>Finally, there are a few other common retrieve or replace operations
@@ -2297,8 +2252,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="tip-whats-the-difference-between-the-in-and-the-operators" class="callout-inner">
 <h3 class="callout-title">Tip: What’s the difference between the
-<code>%in% and the</code>==` operators?<a class="anchor" aria-label="anchor" href="#tip-whats-the-difference-between-the-in-and-the-operators"></a>
-</h3>
+<code>%in% and the</code>==` operators?</h3>
 <div class="callout-content">
 <p>The <code>%in%</code> operator is used to test if the elements of a
 vector are present in another vector. In the example above, if both
@@ -2325,8 +2279,7 @@ <h3 class="callout-title">Tip: What’s the difference between the
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-1" class="callout-inner">
-<h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor" href="#review-exercise-1"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 1</h3>
 <div class="callout-content">
 <p>What data modes are the following vectors? a. <code>snps</code><br>
 b. <code>snp_chromosomes</code><br>
@@ -2383,8 +2336,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-2" class="callout-inner">
-<h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor" href="#review-exercise-2"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 2</h3>
 <div class="callout-content">
 <p>Add the following values to the specified vectors: a. To the
 <code>snps</code> vector add: “rs662799”<br>
@@ -2445,8 +2397,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-3" class="callout-inner">
-<h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor" href="#review-exercise-3"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 3</h3>
 <div class="callout-content">
 <p>Make the following change to the <code>snp_genes</code> vector:</p>
 <p>Hint: Your vector should look like this in ‘Environment’:
@@ -2492,8 +2443,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-4" class="callout-inner">
-<h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor" href="#review-exercise-4"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 4</h3>
 <div class="callout-content">
 <p>Using indexing, create a new vector named <code>combined</code> that
 contains:</p>
@@ -2538,8 +2488,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-5" class="callout-inner">
-<h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor" href="#review-exercise-5"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 5</h3>
 <div class="callout-content">
 <p>What type of data is <code>combined</code>?</p>
 </div>
@@ -2572,8 +2521,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="lists" class="callout-inner">
-<h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
-</h3>
+<h3 class="callout-title">Lists</h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
 genomics lessons. That said, you may come across lists in the way that
@@ -2648,8 +2596,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Effectively using R is a journey of months or years. Still you don’t
@@ -2700,7 +2647,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a>
-<a class="anchor" aria-label="anchor" href="#preface"></a>
 </h2>
 <hr class="half-width">
 <p>The Intro to R and RStudio for Genomics is a part of the Genomics
@@ -2720,7 +2666,6 @@ <h3 class="card-title">Objectives</h3>
 </li>
 <li>Dataset publicly available - in this case through the NCBI SRA (<a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">http://www.ncbi.nlm.nih.gov/sra</a>)</li>
 </ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
 </h2>
 <hr class="half-width">
 <p>Microbes are ideal organisms for exploring ‘Long-term Evolution
@@ -2805,7 +2750,6 @@ <h3 class="card-title">Objectives</h3>
 strains?</li>
 <li>What are the base pair changes between strains?</li>
 </ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
-<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
 </h2>
 <hr class="half-width">
 <p>Publicly accessible sequencing files in FASTQ formats can be
@@ -2819,7 +2763,6 @@ <h3 class="card-title">Objectives</h3>
 <img src="fig/variant_calling_workflow.png" alt="variant calling workflow. Sequence reads (FASTQ files), Quality control (FASTQ files), Alignment to Genome (SAM/BAM files), Alignment cleanup (BAM file ready for variant calling), Variant Calling (VCF file)" style="width: 250px;" class="figure">
 </center>
 </section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
-<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
 </h2>
 <hr class="half-width">
 <p>VCF files contain variants that were called against a reference
@@ -2976,7 +2919,6 @@ <h3 class="card-title">Objectives</h3>
 <p>For more information on VCF files visit The Broad Institute’s <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" class="external-link">VCF
 guide</a>.</p>
 </section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -2998,8 +2940,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The dataset comes from a real world experiment in E. coli.</li>
@@ -3063,7 +3004,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
-<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
 </h2>
 <hr class="half-width">
 <p>A substantial amount of the data we work with in genomics will be
@@ -3101,8 +3041,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-keep-your-raw-data-separate" class="callout-inner">
-<h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
-</h3>
+<h3 class="callout-title">Tip: Keep your raw data separate</h3>
 <div class="callout-content">
 <p>When you work with data in R, you are not changing the original file
 you loaded that data from. This is different than (for example) working
@@ -3115,7 +3054,6 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 </div>
 </section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
-<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
 </h2>
 <hr class="half-width">
 <p>There are several ways to import data into R. For our purpose here,
@@ -3129,8 +3067,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 <div id="exercise-review-the-arguments-of-the-read.csv-function" class="callout-inner">
 <h3 class="callout-title">Exercise: Review the arguments of the
-<code>read.csv()</code> function<a class="anchor" aria-label="anchor" href="#exercise-review-the-arguments-of-the-read.csv-function"></a>
-</h3>
+<code>read.csv()</code> function</h3>
 <div class="callout-content">
 <p><strong>Before using the <code>read.csv()</code> function, use R’s
 help feature to answer the following questions</strong>.</p>
@@ -3157,7 +3094,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li><p>The <code>read.csv()</code> function has the argument ‘header’
@@ -3186,8 +3123,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
-<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
-</h3>
+<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?</h3>
 <div class="callout-content">
 <p>The reason for this is because <code>read.csv</code> is actually a
 short cut for <code>read.table("file.csv", sep = ",")</code>. You can
@@ -3227,8 +3163,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 name of the object will open a view of the data in a new tab.</p>
 <figure><img src="%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure></section><section><h2 class="section-heading" id="summarizing-subsetting-and-determining-the-structure-of-a-data-frame-">Summarizing, subsetting, and determining the structure of a data
-frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame."></a>
-<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a>
+frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a>
 </h2>
 <hr class="half-width">
 <p>A <strong>data frame is the standard way in R to store tabular
@@ -3357,8 +3292,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
-</h3>
+<h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
 <div class="callout-content">
 <p>Remeber when we said mode and class are sometimes different? If you
 do, here is a chance to check. What happens when you try the
@@ -3375,7 +3309,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3412,7 +3346,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </li>
 </ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width">
 <p>Factors are the final major data structure we will introduce in our R
@@ -3546,8 +3479,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
-<h3 class="callout-title">Tip: treating objects as categories without changing their mode<a class="anchor" aria-label="anchor" href="#tip-treating-objects-as-categories-without-changing-their-mode"></a>
-</h3>
+<h3 class="callout-title">Tip: treating objects as categories without changing their mode</h3>
 <div class="callout-content">
 <p>You don’t have to make an object a factor to get the benefits of
 treating an object as a factor. See what happens when you use the
@@ -3559,7 +3491,6 @@ <h3 class="callout-title">Tip: treating objects as categories without changing t
 </div>
 </div>
 </section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
-<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
 </h2>
 <hr class="half-width">
 <p>One of the most common uses for factors will be when you plot
@@ -3618,8 +3549,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout-inner">
-<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?<a class="anchor" aria-label="anchor" href="#tip-packages-in-r-what-are-they-and-why-do-we-use-them"></a>
-</h3>
+<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?</h3>
 <div class="callout-content">
 <p>Packages are simply collections of functions and/or data that can be
 used to extend the capabilities of R beyond the core functionality that
@@ -3654,7 +3584,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
 </h2>
 <hr class="half-width">
 <p>Next, we are going to talk about how you can get specific values from
@@ -3670,8 +3599,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-subsetting-a-data-frame" class="callout-inner">
-<h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" aria-label="anchor" href="#exercise-subsetting-a-data-frame"></a>
-</h3>
+<h3 class="callout-title">Exercise: Subsetting a data frame</h3>
 <div class="callout-content">
 <p><strong>Try the following indices and functions and try to figure out
 what they return</strong></p>
@@ -3697,7 +3625,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol>
@@ -4107,7 +4035,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
                                                                      </code></pre>
 </div>
 </section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
 </h2>
 <hr class="half-width">
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout">
@@ -4115,8 +4042,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>While we are going to address coercion in the context of data frames
 most of these methods apply to other data structures, such as
@@ -4311,7 +4237,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
-<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
 </h2>
 <hr class="half-width">
 <p>Lets summarize this section on coercion with a few take home
@@ -4333,8 +4258,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames-1"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>Prior to R 4.0 when importing a data frame using any one of the
 <code>read.table()</code> functions such as <code>read.csv()</code> ,
@@ -4349,7 +4273,6 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
-<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
 </h2>
 <hr class="half-width">
 <p>Here are a few operations that don’t need much explanation, but which
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-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>The <code>order()</code> function lists values in increasing order by
 default. Look at the documentation for this function and change
@@ -4410,7 +4332,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
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 [29] "gt_GT_alleles"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
-<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
 </h2>
 <hr class="half-width">
 <p>We can save data to a file. We will save our
@@ -4469,7 +4390,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 provide a file name, the file will be written in the current working
 directory).</p>
 </section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
-<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
 </h2>
 <hr class="half-width">
 <p>Excel is one of the most common formats, so we need to discuss how to
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-<h3 class="callout-title">Exercise: Putting it all together - data frames<a class="anchor" aria-label="anchor" href="#exercise-putting-it-all-together---data-frames"></a>
-</h3>
+<h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <div class="callout-content">
 <p><strong>Using the <code>Ecoli_metadata</code> data frame created
 above, answer the following questions</strong></p>
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-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>It is easy to import data into R from tabular formats including
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 </div>
 </div>
 <section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
-<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
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 <hr class="half-width">
 <p>So far we have told you about using packages that are included in the
@@ -4716,7 +4633,6 @@ <h3 class="card-title">Objectives</h3>
 analysis of biological data, and that it can be a great place to look
 for tools to help you analyze your -omics datasets!</p>
 </section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
-<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
 </h2>
 <hr class="half-width">
 <p>Since access to the <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> repository is not
@@ -4726,7 +4642,6 @@ <h3 class="card-title">Objectives</h3>
 are working on, but you can use the same approach to install any of the
 many thousands of available packages.</p>
 <figure><img src="fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
-<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
 </h2>
 <hr class="half-width">
 <p>The first step is to install a package that <em>is</em> on CRAN,
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 </div>
 </section><section><h2 class="section-heading" id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager">Second, install the vcfR package from Bioconductor using
-<code>BiocManager</code><a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a>
+<code>BiocManager</code>
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 </h2>
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-</h3>
+<h3 class="callout-title">Head’s Up: Installing vcfR may take a while due to numerous dependencies</h3>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
 can take a while.</p>
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-</h3>
+<h3 class="callout-title">Note: Installing packages from Bioconductor vs from CRAN</h3>
 <div class="callout-content">
 <p>Some packages begin by being available only on Bioconductor, and then
 later move to CRAN. <code>vcfR</code> is one such package, which
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 </div>
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 </section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
-<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
 </h2>
 <hr class="half-width">
 <p>While we are only focusing in this workshop on VCF analyses, there
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-</h3>
+<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website</h3>
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 <p>There are several thousand packages available through the
 Bioconductor website. It can be a bit of a challenge to find what you
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-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul>
 <li>Use the <code>BiocManager::available()</code> function to see what
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-</h3>
+<h3 class="callout-title">Tip: Refreshing the RStudio package view after installing</h3>
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 <p>If you install a package from Bioconductor, you may need to refresh
 the RStudio package view to see it in your list. You can do this by
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 </div>
 </div>
 </section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
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 <i class="callout-icon" data-feather="key"></i>
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 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Bioconductor is an alternative package repository for bioinformatics
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-<h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
-</h3>
+<h3 class="callout-title">Tip: Installing packages</h3>
 <div class="callout-content">
 <p>It may be temping to install the <code>tidyverse</code> package, as
 it contains many useful collection of packages for this lesson and
@@ -5008,7 +4914,6 @@ <h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="
 </div>
 </div>
 <section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
-<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
 </h2>
 <hr class="half-width">
 <p>The package <code>dplyr</code> is a fairly new (2014) package that
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 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Create a table that contains all the columns with the letter “i” and
 column “POS”, without columns “Indiv” and “FILTER”. Hint: look at for a
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 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<em> (continued)</em><a class="anchor" aria-label="anchor" href="#challenge"></a>
+<h3 class="callout-title">Challenge<em> (continued)</em>
 </h3>
 <div class="callout-content">
 <p>We can also get to <code>variants_result</code> in one line of
@@ -5508,8 +5412,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Select all the mutations that occurred between the positions 1e6 (one
 million) and 2e6 (inclusive) that have a QUAL greater than 200, and
@@ -5708,8 +5611,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 <div id="exercise-pipe-and-filter" class="callout-inner">
-<h3 class="callout-title">Exercise: Pipe and filter<a class="anchor" aria-label="anchor" href="#exercise-pipe-and-filter"></a>
-</h3>
+<h3 class="callout-title">Exercise: Pipe and filter</h3>
 <div class="callout-content">
 <p>Starting with the <code>variants</code> data frame, use pipes to
 subset the data to include only observations from SRR2584863 sample,
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 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>There are a lot of columns in our data set, so let’s just look at the
 <code>sample_id</code>, <code>POS</code>, <code>QUAL</code>, and
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 <div class="callout-content">
 <ul>
 <li>How many mutations are INDELs?</li>
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-</h3>
+<h3 class="callout-title">Grouped Data Frames in Tidyverse</h3>
 <div class="callout-content">
 <p>When you group a data frame with <code>group_by()</code>, you get a
 grouped data frame. This is a special type of data frame that has all
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-</h3>
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 <div class="callout-content">
 <ul>
 <li>Use the <code>dplyr</code> package to manipulate data frames.</li>
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 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong><a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
+<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong>
 <a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
 </h2>
 <hr class="half-width">
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 or discrete</a>, a quick way to check is to use the <a href="https://www.geeksforgeeks.org/get-summary-of-results-produced-by-functions-in-r-programming-summary-function/" class="external-link"><code>summary()</code></a>
 function. Continuous variables have descriptive statistics but not the
 discrete variables.</p>
-</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code><a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
+</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code>
 <a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
 </h2>
 <hr class="half-width">
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 has been already loaded along with other packages as part of the
 <strong><code>tidyverse</code></strong> framework.</p>
 </section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
 </h2>
 <hr class="half-width">
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 </div>
 </section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
-<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
 </h2>
 <hr class="half-width">
 <p>Building plots with <strong><code>ggplot2</code></strong> is
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of mapping quality
 (<code>MQ</code>) over position (<code>POS</code>) with the samples
@@ -6780,7 +6675,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="codewrapper sourceCode" id="cb25">
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 <span>  <span class="fu">theme</span><span class="op">(</span>text <span class="op">=</span> <span class="fu">element_text</span><span class="op">(</span>family <span class="op">=</span> <span class="st">"Bookman"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
 </div>
 <figure><img src="fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a>
-<a class="anchor" aria-label="anchor" href="#faceting"></a>
 </h2>
 <hr class="half-width">
 <p><strong><code>ggplot2</code></strong> has a special technique called
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 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of PHRED scaled
 quality (<code>QUAL</code>) over position (<code>POS</code>) with the
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   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6898,7 +6791,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a>
-<a class="anchor" aria-label="anchor" href="#barplots"></a>
 </h2>
 <hr class="half-width">
 <p>We can create barplots using the <a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link"><code>geom_bar</code></a>
@@ -6917,8 +6809,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Since we already have the sample_id labels on the individual plot
 facets, we don’t need the legend. Use the help file for
@@ -6932,7 +6823,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6948,7 +6839,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a>
-<a class="anchor" aria-label="anchor" href="#density"></a>
 </h2>
 <hr class="half-width">
 <p>We can create density plots using the <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
@@ -6968,8 +6858,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-3" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-3"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 to plot the distribution of <code>DP</code> with a different fill for
@@ -6982,7 +6871,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6999,7 +6888,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </section><section><h2 class="section-heading" id="ggplot2-themes">
 <strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
-<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
 </h2>
 <hr class="half-width">
 <p>In addition to <a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link"><code>theme_bw()</code></a>,
@@ -7023,8 +6911,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="challenge-4" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-4"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>With all of this information in hand, please take another five
 minutes to either improve one of the plots generated in this exercise or
@@ -7041,7 +6928,6 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </div>
 </div>
 </section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
-<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
 </h2>
 <hr class="half-width">
 <p><strong><code>ggplot2</code></strong> offers many more informative
@@ -7059,7 +6945,6 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link"><code>geom_violin()</code></a>,
 for violin plots</li>
 </ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
@@ -7080,8 +6965,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>ggplot2 is a powerful tool for high-quality plots</li>
@@ -7129,7 +7013,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
 </h2>
 <hr class="half-width">
 <figure><img src="fig/oreilly_book_covers.png" alt="rstudio default session" style="width: 600px;" class="figure mx-auto d-block"></figure><p>No matter how much experience you have with R, you will find yourself
@@ -7141,7 +7024,6 @@ <h3 class="card-title">Objectives</h3>
 <p>“Never memorize something that you can look up” -- A. Einstein</p>
 </blockquote>
 </section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
-<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
 </h2>
 <hr class="half-width">
 <p>Two popular websites will be of great help with many R problems. For
@@ -7155,8 +7037,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-asking-for-help-using-online-forums" class="callout-inner">
-<h3 class="callout-title">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
-</h3>
+<h3 class="callout-title">Tip: Asking for help using online forums:</h3>
 <div class="callout-content">
 <ul>
 <li>When searching for R help, look for <a href="https://stackoverflow.com/questions/tagged/r" class="external-link">answers with the ‘r’
@@ -7175,7 +7056,6 @@ <h3 class="callout-title">Tip: Asking for help using online forums:<a class="anc
 </div>
 </div>
 </section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
-<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
 </h2>
 <hr class="half-width">
 <p>Often, in order to duplicate the issue you are having, someone may
@@ -7237,7 +7117,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="fu">saveRDS</span><span class="op">(</span><span class="va">iris</span>, file<span class="op">=</span><span class="st">"iris.rds"</span><span class="op">)</span> <span class="co"># By convention, we use the .rds file extension</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
-<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
 </h2>
 <hr class="half-width">
 <p>Finally, here are a few pieces of introductory R knowledge that are
@@ -7300,8 +7179,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>R provides thousands of functions for analyzing data, and provides
@@ -7337,7 +7215,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -7360,8 +7238,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/aio.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/aio.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
-  "datePublished": "2024-08-20"
+  "dateModified": "2024-08-27",
+  "datePublished": "2024-08-27"
 }
 
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diff --git a/assets/styles.css b/assets/styles.css
index 58233a7b..4dc74d32 100644
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.offcanvas-body{display:flex;flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;flex-basis:auto}.navbar-expand .navbar-toggler{display:none}.navbar-expand .offcanvas{position:static;z-index:auto;flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:rgba(0,0,0,0) !important;border:0 !important;transform:none !important;transition:none}.navbar-expand .offcanvas .offcanvas-header{display:none}.navbar-expand .offcanvas .offcanvas-body{display:flex;flex-grow:0;padding:0;overflow-y:visible}.navbar-dark,.navbar[data-bs-theme=dark]{--bs-navbar-color: rgba(255, 255, 255, 0.55);--bs-navbar-hover-color: rgba(255, 255, 255, 0.75);--bs-navbar-disabled-color: rgba(255, 255, 255, 0.25);--bs-navbar-active-color: #fff;--bs-navbar-brand-color: #fff;--bs-navbar-brand-hover-color: #fff;--bs-navbar-toggler-border-color: rgba(255, 255, 255, 0.1);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255, 255, 255, 0.55%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme=dark] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255, 255, 255, 0.55%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: 0.5rem;--bs-card-title-color: 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reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1*var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media(prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath 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var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #0d6efd;--bs-pagination-active-border-color: #0d6efd;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #0d6efd;--bs-progress-bar-transition: width 0.6s ease;display:flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;flex-direction:column;justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #0d6efd;--bs-list-group-active-border-color: #0d6efd;display:flex;flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.5;--bs-btn-close-hover-opacity: 0.75;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;align-items:center;padding:var(--bs-toast-padding-y) 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.nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: 0.5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: 0.3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 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reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1*var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media(prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: 0.5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #0d6efd;--bs-pagination-active-border-color: #0d6efd;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #0d6efd;--bs-progress-bar-transition: width 0.6s ease;display:flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;flex-direction:column;justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #0d6efd;--bs-list-group-active-border-color: #0d6efd;display:flex;flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.5;--bs-btn-close-hover-opacity: 0.75;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(13, 110, 253, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-0.5*var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: 0.5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: var(--bs-box-shadow-sm);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: 0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0, -50px)}@media(prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin)*2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;align-items:center;min-height:calc(100% - var(--bs-modal-margin)*2)}.modal-content{position:relative;display:flex;flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: 0.5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;flex-shrink:0;align-items:center;justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y)*.5) calc(var(--bs-modal-header-padding-x)*.5);margin:calc(-0.5*var(--bs-modal-header-padding-y)) calc(-0.5*var(--bs-modal-header-padding-x)) calc(-0.5*var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;flex-shrink:0;flex-wrap:wrap;align-items:center;justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap)*.5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap)*.5)}@media(min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: var(--bs-box-shadow)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media(min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media(min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media(max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media(max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media(max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media(max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media(max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: 0.5rem;--bs-tooltip-padding-y: 0.25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:0.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: 0.9;--bs-tooltip-arrow-width: 0.8rem;--bs-tooltip-arrow-height: 0.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:rgba(0,0,0,0);border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=top] .tooltip-arrow{bottom:calc(-1*var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=top] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width)*.5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=right] .tooltip-arrow{left:calc(-1*var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=right] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width)*.5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=bottom] .tooltip-arrow{top:calc(-1*var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=bottom] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow{right:calc(-1*var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^=left] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width)*.5) 0 calc(var(--bs-tooltip-arrow-width)*.5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:0.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: var(--bs-border-color-translucent);--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: var(--bs-box-shadow);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: 0.5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: 0.5rem;--bs-popover-arrow-border: var(--bs-popover-border-color);z-index:var(--bs-popover-zindex);display:block;max-width:var(--bs-popover-max-width);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-popover-font-size);word-wrap:break-word;background-color:var(--bs-popover-bg);background-clip:padding-box;border:var(--bs-popover-border-width) solid var(--bs-popover-border-color);border-radius:var(--bs-popover-border-radius)}.popover .popover-arrow{display:block;width:var(--bs-popover-arrow-width);height:var(--bs-popover-arrow-height)}.popover .popover-arrow::before,.popover .popover-arrow::after{position:absolute;display:block;content:"";border-color:rgba(0,0,0,0);border-style:solid;border-width:0}.bs-popover-top>.popover-arrow,.bs-popover-auto[data-popper-placement^=top]>.popover-arrow{bottom:calc(-1*(var(--bs-popover-arrow-height)) - var(--bs-popover-border-width))}.bs-popover-top>.popover-arrow::before,.bs-popover-auto[data-popper-placement^=top]>.popover-arrow::before,.bs-popover-top>.popover-arrow::after,.bs-popover-auto[data-popper-placement^=top]>.popover-arrow::after{border-width:var(--bs-popover-arrow-height) calc(var(--bs-popover-arrow-width)*.5) 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+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
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   "identifier": "https://datacarpentry.github.io/genomics-r-intro/discuss.html",
   "dateCreated": "2018-03-12",
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@@ -522,7 +522,7 @@ <h3 id="07-r-help-figure-1">Figure 1</h3>
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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/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 		</footer>
 </div> <!-- / div.container -->
@@ -545,8 +545,8 @@ <h3 id="07-r-help-figure-1">Figure 1</h3>
   "url": "https://datacarpentry.github.io/genomics-r-intro/images.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/images.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
-  "datePublished": "2024-08-20"
+  "dateModified": "2024-08-27",
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index d310c5c4..4cb5d4ff 100644
--- a/index.html
+++ b/index.html
@@ -292,10 +292,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -315,7 +315,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -380,8 +380,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="prerequisites" class="callout-inner">
-<h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" href="#prerequisites"></a>
-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>
 <strong>Experimenter’s Mindset</strong>: We define the
@@ -412,12 +411,10 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 option B below where you will only need to <a href="https://figshare.com/articles/Data_Carpentry_Genomics_beta_2_0/7726454" class="external-link">download
 the data files</a> to your local working directory where you will create
 the r-project in.</p>
-<section><h2 class="section-heading" id="r-genomics-workshop-setup-directions">R Genomics workshop setup directions<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a>
-<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a></h2>
+<section><h2 class="section-heading" id="r-genomics-workshop-setup-directions">R Genomics workshop setup directions<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a></h2>
 <hr class="half-width"><p>For general setup for the genomics lessons, see that page of <a href="https://datacarpentry.org/genomics-workshop/" class="external-link">the genomics
 workshop</a>.</p>
-</section><section><h2 class="section-heading" id="installing-r">Installing R<a class="anchor" aria-label="anchor" href="#installing-r"></a>
-<a class="anchor" aria-label="anchor" href="#installing-r"></a></h2>
+</section><section><h2 class="section-heading" id="installing-r">Installing R<a class="anchor" aria-label="anchor" href="#installing-r"></a></h2>
 <hr class="half-width"><p>This workshop is designed to be run on pre-imaged Amazon Web Services
 (AWS) instances. With the exception of a spreadsheet program, all of the
 software and data used in the workshop are hosted on an Amazon. However,
@@ -475,8 +472,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="installing-rstudio">Installing RStudio<a class="anchor" aria-label="anchor" href="#installing-rstudio"></a>
-<a class="anchor" aria-label="anchor" href="#installing-rstudio"></a></h2>
+</section><section><h2 class="section-heading" id="installing-rstudio">Installing RStudio<a class="anchor" aria-label="anchor" href="#installing-rstudio"></a></h2>
 <hr class="half-width"><p>The RStudio integrated development environment (IDE) is a popular way
 to use R. We will cover what RStudio is in the lesson. All operating
 systems can go to the Posit LLC <a href="https://posit.co/download/rstudio-desktop/" class="external-link">download pages</a> to
@@ -510,7 +506,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -532,8 +528,8 @@ <h3 class="accordion-header" id="headingSpoiler3">
   "url": "https://datacarpentry.github.io/genomics-r-intro/index.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/index.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
-  "datePublished": "2024-08-20"
+  "dateModified": "2024-08-27",
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 430d2e6a..bca67a27 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -342,10 +342,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
             </div>
 
             <hr class="half-width">
-<div class="accordion accordion-flush resources" id="accordionFlush12">
+<div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources">
+            <hr class="half-width lesson-resources">
 <a href="aio.html">See all in one page</a>
 
 
@@ -419,7 +419,7 @@ <h1>Instructor Notes</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -442,8 +442,8 @@ <h1>Instructor Notes</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor-notes.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
-  "datePublished": "2024-08-20"
+  "dateModified": "2024-08-27",
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/00-introduction.html b/instructor/00-introduction.html
index 34680c4e..ea50f859 100644
--- a/instructor/00-introduction.html
+++ b/instructor/00-introduction.html
@@ -301,10 +301,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -324,7 +324,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -403,8 +403,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
-<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a></h2>
+<section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a></h2>
 <hr class="half-width"><p>In this lesson we will take you through the very first things you
 need to get R working.</p>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout">
@@ -412,8 +411,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anchor" aria-label="anchor" href="#tip-this-lesson-works-best-on-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: This lesson works best on the cloud</h3>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
 virtual machine instances provided to you at a genomics workshop. Much
@@ -425,16 +423,14 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
-<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a></h2>
+</section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a></h2>
 <hr class="half-width"><p><a href="https://en.wikipedia.org/wiki/R_(programming_language)" class="external-link">The
 programming language R</a> has been around since 1995, and was created
 by Ross Ihaka and Robert Gentleman at the University of Auckland, New
 Zealand. R is based off the S programming language developed at Bell
 Labs and was developed to teach intro statistics. See this <a href="https://www.stat.auckland.ac.nz/~ihaka/downloads/Massey.pdf" class="external-link">slide
 deck</a> by Ross Ihaka for more info on the subject.</p>
-</section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
-<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a></h2>
+</section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a></h2>
 <hr class="half-width"><p>At more than 20 years old, R is fairly mature and <a href="https://www.tiobe.com/tiobe-index/r/" class="external-link">growing in popularity</a>.
 However, programming isn’t a popularity contest. Here are key advantages
 of analyzing data in R:</p>
@@ -464,8 +460,7 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="discussion-your-experience" class="callout-inner">
-<h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-label="anchor" href="#discussion-your-experience"></a>
-</h3>
+<h3 class="callout-title">Discussion: Your experience</h3>
 <div class="callout-content">
 <p>What has motivated you to learn R? Have you had a research question
 for which spreadsheet programs such as Excel have proven difficult to
@@ -473,8 +468,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a></h2>
+</section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a></h2>
 <hr class="half-width"><p>In these lessons, we will be making use of a software called <a href="https://www.rstudio.com/products/RStudio/" class="external-link">RStudio</a>, an <a href="https://en.wikipedia.org/wiki/Integrated_development_environment" class="external-link">Integrated
 Development Environment (IDE)</a>. RStudio, like most IDEs, provides a
 graphical interface to R, making it more user-friendly, and providing
@@ -484,8 +478,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 Server</a>, a version of RStudio that can be accessed in your web
 browser. RStudio Server has the same features of the Desktop version of
 RStudio you could download as standalone software.</p>
-</section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a></h2>
+</section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a></h2>
 <hr class="half-width"><p>Open a web browser and enter the URL you used to log in at the
 terminal (provided by your instructors), followed by <code>:8787</code>.
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
@@ -496,8 +489,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout-inner">
-<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.<a class="anchor" aria-label="anchor" href="#tip-make-sure-there-are-no-spaces-before-or-after-your-url."></a>
-</h3>
+<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.</h3>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -510,8 +502,7 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 credentials for the genomics Data Carpentry instances will be provided
 by your instructors.</p>
 <p>You should now see the RStudio interface:</p>
-<figure><img src="../fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
-<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a></h2>
+<figure><img src="../fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a></h2>
 <hr class="half-width"><p>One of the first benefits we will take advantage of in RStudio is
 something called an <strong>RStudio Project</strong>. An RStudio project
 allows you to more easily:</p>
@@ -551,8 +542,7 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-your-project-more-reproducible-with-renv" class="callout-inner">
-<h3 class="callout-title">Tip: Make your project more reproducible with renv<a class="anchor" aria-label="anchor" href="#tip-make-your-project-more-reproducible-with-renv"></a>
-</h3>
+<h3 class="callout-title">Tip: Make your project more reproducible with renv</h3>
 <div class="callout-content">
 <p>One of the most wonderful and also frustrating aspects of working
 with R is managing packages. We will talk more about them, but packages
@@ -570,8 +560,7 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a>
-<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a></h2>
+</section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a></h2>
 <hr class="half-width"><p>Now that we are ready to start exploring R, we will want to keep a
 record of the commands we are using. To do this we can create an R
 script:</p>
@@ -589,16 +578,14 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-save-your-script-now" class="callout-inner">
-<h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label="anchor" href="#tip-save-your-script-now"></a>
-</h3>
+<h3 class="callout-title">Tip: Save your script now</h3>
 <div class="callout-content">
 <p>Remember to save your script at this point. Anything can happen
 during your lesson and you don’t want to lose your work!</p>
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a>
-<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a></h2>
+</section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a></h2>
 <hr class="half-width"><p>Here are the major windows (or panes) of the RStudio environment:</p>
 <figure><img src="../fig/rstudio_session_4pane_layout.png" alt="rstudio default session" style="width: 1000px;" class="figure mx-auto d-block"></figure><ul><li>
 <strong>Source</strong>: This pane is where you will write/view R
@@ -635,8 +622,7 @@ <h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label=
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-uploads-and-downloads-in-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: Uploads and downloads in the cloud</h3>
 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
 cloud instance (click the “more” button) to your local computer. Uploads
@@ -655,8 +641,7 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="you-are-working-with-r" class="callout-inner">
-<h3 class="callout-title">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a>
-</h3>
+<h3 class="callout-title">You are working with R</h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
 of reasons to. For example, once you have written an RScript, you can
@@ -667,8 +652,7 @@ <h3 class="callout-title">You are working with R<a class="anchor" aria-label="an
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
-<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a></h2>
+</section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a></h2>
 <hr class="half-width"><p>Now that we have covered the more aesthetic aspects of RStudio, we
 can get to work using some commands. We will write, execute, and save
 the commands we learn in our <strong>genomics_r_basics.R</strong> script
@@ -710,8 +694,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-work-interactively-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" aria-label="anchor" href="#exercise-work-interactively-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Work interactively in R</h3>
 <div class="callout-content">
 <p>What happens when you try to enter the <code>getwd()</code> command
 in the Console pane?</p>
@@ -770,7 +753,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-never-use-setwd" class="callout-inner">
-<h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
+<h3 class="callout-title">Tip: Never use <code>setwd()</code>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -787,8 +770,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
-<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a></h2>
+</section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a></h2>
 <hr class="half-width"><p>A function in R (or any computing language) is a short program that
 takes some input and returns some output. Functions may seem like an
 advanced topic (and they are), but you have already used at least one
@@ -799,8 +781,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-what-do-these-functions-do" class="callout-inner">
-<h3 class="callout-title">Exercise: What do these functions do?<a class="anchor" aria-label="anchor" href="#exercise-what-do-these-functions-do"></a>
-</h3>
+<h3 class="callout-title">Exercise: What do these functions do?</h3>
 <div class="callout-content">
 <p>Try the following functions by writing them in your script. See if
 you can guess what they do, and make sure to add comments to your script
@@ -855,8 +836,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] 3</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a></h2>
+</section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a></h2>
 <hr class="half-width"><p>What if you wanted to round to one significant digit?
 <code>round()</code> can do this, but you may first need to read the
 help to find out how. To see the help (In R sometimes also called a
@@ -945,8 +925,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-searching-for-r-functions" class="callout-inner">
-<h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" aria-label="anchor" href="#exercise-searching-for-r-functions"></a>
-</h3>
+<h3 class="callout-title">Exercise: Searching for R functions</h3>
 <div class="callout-content">
 <p>Use <code>help.search()</code> to find R functions for the following
 statistical functions. Remember to put your search query in quotes
@@ -983,8 +962,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 important ones are <a href="https://cran.r-project.org/" class="external-link">CRAN</a> - the
 main repository for R, and <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> - a popular repository
 for bioinformatics-related R packages.</p>
-</section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
-<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a></h2>
+</section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a></h2>
 <hr class="half-width"><p>Here is one last bonus we will mention about RStudio. It’s difficult
 to remember all of the arguments and definitions associated with a given
 function. When you start typing the name of a function and hit the
@@ -998,8 +976,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>R is a powerful, popular open-source scripting language</li>
 <li>You can customize the layout of RStudio, and use the project feature
@@ -1045,7 +1022,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1068,7 +1045,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/00-introduction.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/01-r-basics.html b/instructor/01-r-basics.html
index dc7686e8..943de4b7 100644
--- a/instructor/01-r-basics.html
+++ b/instructor/01-r-basics.html
@@ -302,10 +302,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -325,7 +325,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -400,8 +400,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r">“The fantastic world of R awaits you” OR “Nobody wants to learn how
-to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
-<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a></h2>
+to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a></h2>
 <hr class="half-width"><p>Before we begin this lesson, we want you to be clear on the goal of
 the workshop and these lessons. We believe that every learner can
 <strong>achieve competency with R</strong>. You have reached competency
@@ -414,8 +413,7 @@ <h3 class="card-title">Objectives</h3>
 get, the more complex the analyses you will be able to carry out, with
 less frustration, and in less time - the fantastic world of R awaits
 you!</p>
-</section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
-<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a></h2>
+</section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a></h2>
 <hr class="half-width"><p>Nobody wants to learn how to use R. People want to learn how to use R
 to analyze their own research questions! Ok, maybe some folks learn R
 for R’s sake, but these lessons assume that you want to start analyzing
@@ -441,8 +439,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-where-to-learn-more" class="callout-inner">
-<h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
-</h3>
+<h3 class="callout-title">Tip: Where to learn more</h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
 them can be quite technical, but if you are a regular R user you may
@@ -472,15 +469,13 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a></h2>
+</section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a></h2>
 <hr class="half-width"><div id="reminder" class="callout prereq">
 <div class="callout-square">
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="reminder" class="callout-inner">
-<h3 class="callout-title">Reminder<a class="anchor" aria-label="anchor" href="#reminder"></a>
-</h3>
+<h3 class="callout-title">Reminder</h3>
 <div class="callout-content">
 <p>At this point you should be coding along in the
 “<strong>genomics_r_basics.R</strong>” script we created in the last
@@ -539,8 +534,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-some-objects-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" aria-label="anchor" href="#exercise-create-some-objects-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create some objects in R</h3>
 <div class="callout-content">
 <p>Create the following objects; give each object an appropriate name
 (your best guess at what name to use is fine):</p>
@@ -574,8 +568,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a></h2>
+</section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a></h2>
 <hr class="half-width"><p>Here are some important details about naming objects in R.</p>
 <ul><li>
 <strong>Avoid spaces and special characters</strong>: Object names
@@ -618,8 +611,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout-inner">
-<h3 class="callout-title">Tip: Pay attention to warnings in the script console<a class="anchor" aria-label="anchor" href="#tip-pay-attention-to-warnings-in-the-script-console"></a>
-</h3>
+<h3 class="callout-title">Tip: Pay attention to warnings in the script console</h3>
 <div class="callout-content">
 <p>If you enter a line of code in your script that contains an error,
 RStudio may give you an error message and underline this mistake.
@@ -632,8 +624,7 @@ <h3 class="callout-title">Tip: Pay attention to warnings in the script console<a
 <figure><img src="../fig/rstudio_script_warning.png" alt="rstudio script warning" style="width: 600px;" class="figure mx-auto d-block"></figure></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
-<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a></h2>
+</section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a></h2>
 <hr class="half-width"><p>Once an object has a value, you can change that value by overwriting
 it. R will not give you a warning or error if you overwriting an object,
 which may or may not be a good thing depending on how you look at
@@ -663,8 +654,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 </h3>
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
-<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a></h2>
+</section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a></h2>
 <hr class="half-width"><p>In R, <strong>every object has several properties</strong>:</p>
 <ul><li>
 <strong>Length</strong>: How many distinct values are held in that
@@ -684,8 +674,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-classess-vs.-modes" class="callout-inner">
-<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
-</h3>
+<h3 class="callout-title">Tip: Classess vs. modes</h3>
 <div class="callout-content">
 <p>The difference between modes and classes is a bit
 <strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
@@ -734,8 +723,7 @@ <h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-modes" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their modes<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-modes"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their modes</h3>
 <div class="callout-content">
 <p>Create the following objects in R, then use the <code>mode()</code>
 function to verify their modes. Try to guess what the mode will be
@@ -819,8 +807,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their class using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their class using “class”</h3>
 <div class="callout-content">
 <p>Using the objects created in the previous challenge, use the
 <code>class()</code> function to check their classes.</p>
@@ -930,8 +917,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
-<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a></h2>
+</section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a></h2>
 <hr class="half-width"><p>Once an object exists (which by definition also means it has a mode),
 R can appropriately manipulate that object. For example, objects of the
 numeric modes can be added, multiplied, divided, etc. R provides several
@@ -984,8 +970,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-compute-the-golden-ratio" class="callout-inner">
-<h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" aria-label="anchor" href="#exercise-compute-the-golden-ratio"></a>
-</h3>
+<h3 class="callout-title">Exercise: Compute the golden ratio</h3>
 <div class="callout-content">
 <p>One approximation of the golden ratio (φ) can be found by taking the
 sum of 1 and the square root of 5, and dividing by 2 as in the example
@@ -1018,8 +1003,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a>
-<a class="anchor" aria-label="anchor" href="#vectors"></a></h2>
+</section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a></h2>
 <hr class="half-width"><p>Vectors are probably the most used commonly used object type in R.
 <strong>A vector is a collection of values that are all of the same type
 (numbers, characters, etc.)</strong>. One of the most common ways to
@@ -1078,8 +1062,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 with later in this lesson, data frames, are collections of vectors. What
 we learn here about vectors will pay off even more when we start working
 with data frames.</p>
-</section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a></h2>
+</section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a></h2>
 <hr class="half-width"><p>Let’s create a few more vectors to play around with:</p>
 <div class="codewrapper sourceCode" id="cb44">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1158,8 +1141,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a></h2>
+</section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a></h2>
 <hr class="half-width"><p>Once you have an existing vector, you may want to add a new item to
 it. To do so, you can use the <code>c()</code> function again to add
 your new value:</p>
@@ -1229,8 +1211,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-examining-and-subsetting-vectors" class="callout-inner">
-<h3 class="callout-title">Exercise: Examining and subsetting vectors<a class="anchor" aria-label="anchor" href="#exercise-examining-and-subsetting-vectors"></a>
-</h3>
+<h3 class="callout-title">Exercise: Examining and subsetting vectors</h3>
 <div class="callout-content">
 <p>Answer the following questions to test your knowledge of vectors</p>
 <p>Which of the following are true of vectors in R? A) All vectors have
@@ -1264,8 +1245,7 @@ <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
-<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a></h2>
+</section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a></h2>
 <hr class="half-width"><p>There is one last set of cool subsetting capabilities we want to
 introduce. It is possible within R to retrieve items in a vector based
 on a logical evaluation or numerical comparison. For example, let’s say
@@ -1311,8 +1291,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-magic-of-programming" class="callout-inner">
-<h3 class="callout-title">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
-</h3>
+<h3 class="callout-title">The magic of programming</h3>
 <div class="callout-content">
 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
@@ -1389,8 +1368,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
-<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a></h2>
+</section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a></h2>
 <hr class="half-width"><p>Finally, there are a few other common retrieve or replace operations
 you may want to know about. First, you can check to see if any of the
 values of your vector are missing (i.e. are <code>NA</code>, that stands
@@ -1438,8 +1416,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="tip-whats-the-difference-between-the-in-and-the-operators" class="callout-inner">
 <h3 class="callout-title">Tip: What’s the difference between the
-<code>%in% and the</code>==` operators?<a class="anchor" aria-label="anchor" href="#tip-whats-the-difference-between-the-in-and-the-operators"></a>
-</h3>
+<code>%in% and the</code>==` operators?</h3>
 <div class="callout-content">
 <p>The <code>%in%</code> operator is used to test if the elements of a
 vector are present in another vector. In the example above, if both
@@ -1466,8 +1443,7 @@ <h3 class="callout-title">Tip: What’s the difference between the
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-1" class="callout-inner">
-<h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor" href="#review-exercise-1"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 1</h3>
 <div class="callout-content">
 <p>What data modes are the following vectors? a. <code>snps</code><br>
 b. <code>snp_chromosomes</code><br>
@@ -1524,8 +1500,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-2" class="callout-inner">
-<h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor" href="#review-exercise-2"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 2</h3>
 <div class="callout-content">
 <p>Add the following values to the specified vectors: a. To the
 <code>snps</code> vector add: “rs662799”<br>
@@ -1586,8 +1561,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-3" class="callout-inner">
-<h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor" href="#review-exercise-3"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 3</h3>
 <div class="callout-content">
 <p>Make the following change to the <code>snp_genes</code> vector:</p>
 <p>Hint: Your vector should look like this in ‘Environment’:
@@ -1630,8 +1604,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-4" class="callout-inner">
-<h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor" href="#review-exercise-4"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 4</h3>
 <div class="callout-content">
 <p>Using indexing, create a new vector named <code>combined</code> that
 contains:</p>
@@ -1674,8 +1647,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-5" class="callout-inner">
-<h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor" href="#review-exercise-5"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 5</h3>
 <div class="callout-content">
 <p>What type of data is <code>combined</code>?</p>
 </div>
@@ -1708,8 +1680,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="lists" class="callout-inner">
-<h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
-</h3>
+<h3 class="callout-title">Lists</h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
 genomics lessons. That said, you may come across lists in the way that
@@ -1784,8 +1755,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Effectively using R is a journey of months or years. Still you don’t
 have to be an expert to use R and you can start using and analyzing your
@@ -1834,7 +1804,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1857,7 +1827,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/01-r-basics.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/02-data-prelude.html b/instructor/02-data-prelude.html
index 684d90f3..8fa302f9 100644
--- a/instructor/02-data-prelude.html
+++ b/instructor/02-data-prelude.html
@@ -294,10 +294,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -317,7 +317,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -385,8 +385,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a>
-<a class="anchor" aria-label="anchor" href="#preface"></a></h2>
+<section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a></h2>
 <hr class="half-width"><p>The Intro to R and RStudio for Genomics is a part of the Genomics
 Data Carpentry lessons. In this lesson we will learn the necessary skill
 sets for R and RStudio and apply them directly to a real next-generation
@@ -402,8 +401,7 @@ <h3 class="card-title">Objectives</h3>
 to characterize changes in sequence <em>a priori</em>
 </li>
 <li>Dataset publicly available - in this case through the NCBI SRA (<a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">http://www.ncbi.nlm.nih.gov/sra</a>)</li>
-</ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a></h2>
+</ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a></h2>
 <hr class="half-width"><p>Microbes are ideal organisms for exploring ‘Long-term Evolution
 Experiments’ (LTEEs) - thousands of generations can be generated and
 stored in a way that would be virtually impossible for more complex
@@ -463,8 +461,7 @@ <h3 class="card-title">Objectives</h3>
 <ul><li>How many base pair changes are there between the Cit+ and Cit-
 strains?</li>
 <li>What are the base pair changes between strains?</li>
-</ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
-<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a></h2>
+</ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a></h2>
 <hr class="half-width"><p>Publicly accessible sequencing files in FASTQ formats can be
 downloaded from NCBI SRA. However, at FASTQ files contain unaligned
 sequences of varying quality, and requires clean up and alignment steps
@@ -474,8 +471,7 @@ <h3 class="card-title">Objectives</h3>
 bioinformatics tools that are used:</p>
 <center>
 <img src="../fig/variant_calling_workflow.png" alt="variant calling workflow. Sequence reads (FASTQ files), Quality control (FASTQ files), Alignment to Genome (SAM/BAM files), Alignment cleanup (BAM file ready for variant calling), Variant Calling (VCF file)" style="width: 250px;" class="figure"></center>
-</section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
-<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a></h2>
+</section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a></h2>
 <hr class="half-width"><p>VCF files contain variants that were called against a reference
 genome. These files are slightly more complicated than regular tables
 you can open using programs like Excel and contain two sections: header
@@ -573,8 +569,7 @@ <h3 class="card-title">Objectives</h3>
 <td>the Phred-scaled confidence for the genotype</td>
 </tr></tbody></table><p>For more information on VCF files visit The Broad Institute’s <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" class="external-link">VCF
 guide</a>.</p>
-</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+</section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
 <hr class="half-width"><p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
 Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D,
 Lenski RE. Tempo and mode of genome evolution in a 50,000-generation
@@ -592,8 +587,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>The dataset comes from a real world experiment in E. coli.</li>
 <li>Publicly available FASTQ files can be downloaded from NCBI SRA.</li>
@@ -639,7 +633,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -662,7 +656,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/02-data-prelude.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/03-basics-factors-dataframes.html b/instructor/03-basics-factors-dataframes.html
index 3de43781..f8636089 100644
--- a/instructor/03-basics-factors-dataframes.html
+++ b/instructor/03-basics-factors-dataframes.html
@@ -301,10 +301,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -324,7 +324,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -408,8 +408,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
-<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a></h2>
+<section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a></h2>
 <hr class="half-width"><p>A substantial amount of the data we work with in genomics will be
 tabular data, this is data arranged in rows and columns - also known as
 spreadsheets. We could write a whole lesson on how to work with
@@ -445,8 +444,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-keep-your-raw-data-separate" class="callout-inner">
-<h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
-</h3>
+<h3 class="callout-title">Tip: Keep your raw data separate</h3>
 <div class="callout-content">
 <p>When you work with data in R, you are not changing the original file
 you loaded that data from. This is different than (for example) working
@@ -458,8 +456,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
-<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a></h2>
+</section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a></h2>
 <hr class="half-width"><p>There are several ways to import data into R. For our purpose here,
 we will focus on using the tools every R installation comes with (so
 called “base” R) to import a comma-delimited file containing the results
@@ -471,8 +468,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 <div id="exercise-review-the-arguments-of-the-read.csv-function" class="callout-inner">
 <h3 class="callout-title">Exercise: Review the arguments of the
-<code>read.csv()</code> function<a class="anchor" aria-label="anchor" href="#exercise-review-the-arguments-of-the-read.csv-function"></a>
-</h3>
+<code>read.csv()</code> function</h3>
 <div class="callout-content">
 <p><strong>Before using the <code>read.csv()</code> function, use R’s
 help feature to answer the following questions</strong>.</p>
@@ -497,7 +493,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
@@ -524,8 +520,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
-<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
-</h3>
+<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?</h3>
 <div class="callout-content">
 <p>The reason for this is because <code>read.csv</code> is actually a
 short cut for <code>read.table("file.csv", sep = ",")</code>. You can
@@ -565,8 +560,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 name of the object will open a view of the data in a new tab.</p>
 <figure><img src="../%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure></section><section><h2 class="section-heading" id="summarizing-subsetting-and-determining-the-structure-of-a-data-frame-">Summarizing, subsetting, and determining the structure of a data
-frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame."></a>
-<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a></h2>
+frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a></h2>
 <hr class="half-width"><p>A <strong>data frame is the standard way in R to store tabular
 data</strong>. A data fame could also be thought of as a collection of
 vectors, all of which have the same length. Using only two functions, we
@@ -692,8 +686,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
-</h3>
+<h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
 <div class="callout-content">
 <p>Remeber when we said mode and class are sometimes different? If you
 do, here is a chance to check. What happens when you try the
@@ -708,7 +701,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
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 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -744,8 +737,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </li>
-</ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-factors"></a></h2>
+</ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a></h2>
 <hr class="half-width"><p>Factors are the final major data structure we will introduce in our R
 genomics lessons. Factors can be thought of as vectors which are
 specialized for categorical data. Given R’s specialization for
@@ -877,8 +869,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Tip: treating objects as categories without changing their mode</h3>
 <div class="callout-content">
 <p>You don’t have to make an object a factor to get the benefits of
 treating an object as a factor. See what happens when you use the
@@ -889,8 +880,7 @@ <h3 class="callout-title">Tip: treating objects as categories without changing t
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
-<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a></h2>
+</section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a></h2>
 <hr class="half-width"><p>One of the most common uses for factors will be when you plot
 categorical values. For example, suppose we want to know how many of our
 variants had each possible SNP we could generate a plot:</p>
@@ -945,8 +935,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
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-</h3>
+<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?</h3>
 <div class="callout-content">
 <p>Packages are simply collections of functions and/or data that can be
 used to extend the capabilities of R beyond the core functionality that
@@ -980,8 +969,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a></h2>
+</section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a></h2>
 <hr class="half-width"><p>Next, we are going to talk about how you can get specific values from
 data frames, and where necessary, change the mode of a column of
 values.</p>
@@ -995,8 +983,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-subsetting-a-data-frame" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Exercise: Subsetting a data frame</h3>
 <div class="callout-content">
 <p><strong>Try the following indices and functions and try to figure out
 what they return</strong></p>
@@ -1020,7 +1007,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol><div class="codewrapper sourceCode" id="cb30">
@@ -1415,15 +1402,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
                                        Max.   :1
                                                                      </code></pre>
 </div>
-</section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a></h2>
+</section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a></h2>
 <hr class="half-width"><div id="tip-coercion-isnt-limited-to-data-frames" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>While we are going to address coercion in the context of data frames
 most of these methods apply to other data structures, such as
@@ -1617,8 +1602,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
-<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a></h2>
+</section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a></h2>
 <hr class="half-width"><p>Lets summarize this section on coercion with a few take home
 messages.</p>
 <ul><li>When you explicitly coerce one data type into another (this is known
@@ -1636,8 +1620,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames-1"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>Prior to R 4.0 when importing a data frame using any one of the
 <code>read.table()</code> functions such as <code>read.csv()</code> ,
@@ -1651,8 +1634,7 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
-<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a></h2>
+</section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a></h2>
 <hr class="half-width"><p>Here are a few operations that don’t need much explanation, but which
 are good to know.</p>
 <p>There are lots of arithmetic functions you may want to apply to your
@@ -1696,8 +1678,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>The <code>order()</code> function lists values in increasing order by
 default. Look at the documentation for this function and change
@@ -1711,7 +1692,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1751,8 +1732,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [25] "MQ"            "Indiv"         "gt_PL"         "gt_GT"
 [29] "gt_GT_alleles"</code></pre>
 </div>
-</section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
-<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a></h2>
+</section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a></h2>
 <hr class="half-width"><p>We can save data to a file. We will save our
 <code>SRR2584863_variants</code> object to a .csv file using the
 <code>write.csv()</code> function:</p>
@@ -1767,8 +1747,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 to write to file, and give a path to a file name in quotes (if you only
 provide a file name, the file will be written in the current working
 directory).</p>
-</section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
-<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a></h2>
+</section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a></h2>
 <hr class="half-width"><p>Excel is one of the most common formats, so we need to discuss how to
 make these files play nicely with R. The simplest way to import data
 from Excel is to <strong>save your Excel file in .csv format</strong>*.
@@ -1831,8 +1810,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-putting-it-all-together---data-frames" class="callout-inner">
-<h3 class="callout-title">Exercise: Putting it all together - data frames<a class="anchor" aria-label="anchor" href="#exercise-putting-it-all-together---data-frames"></a>
-</h3>
+<h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <div class="callout-content">
 <p><strong>Using the <code>Ecoli_metadata</code> data frame created
 above, answer the following questions</strong></p>
@@ -1860,7 +1838,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data frames<a clas
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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 <div class="codewrapper sourceCode" id="cb91">
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 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>It is easy to import data into R from tabular formats including
 Excel. However, you still need to check that R has imported and
@@ -1989,7 +1966,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 	<div id="to-top">
@@ -2012,7 +1989,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
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+  "datePublished": "2024-08-27"
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diff --git a/instructor/04-bioconductor-vcfr.html b/instructor/04-bioconductor-vcfr.html
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+++ b/instructor/04-bioconductor-vcfr.html
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               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
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-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
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-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -389,8 +389,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
-<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a></h2>
+<section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a></h2>
 <hr class="half-width"><p>So far we have told you about using packages that are included in the
 base installation of R (this is what comes with R ‘out of the box’), and
 packages that you can install from <a href="https://cran.r-project.org/" class="external-link">CRAN</a> (the Comprehensive R Archive
@@ -405,16 +404,14 @@ <h3 class="card-title">Objectives</h3>
 all of the packages available on Bioconductor are focused on the
 analysis of biological data, and that it can be a great place to look
 for tools to help you analyze your -omics datasets!</p>
-</section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
-<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a></h2>
+</section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a></h2>
 <hr class="half-width"><p>Since access to the <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> repository is not
 built in to base R ‘out of the box’, there are a couple steps needed to
 install packages from this alternative source. We will work through the
 steps (only 2!) to install a package to help with the VCF analysis we
 are working on, but you can use the same approach to install any of the
 many thousands of available packages.</p>
-<figure><img src="../fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
-<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a></h2>
+<figure><img src="../fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a></h2>
 <hr class="half-width"><p>The first step is to install a package that <em>is</em> on CRAN,
 <code>BiocManager</code>. This package will allow us to use it to
 install packages from Bioconductor. You can think of Bioconductor kind
@@ -440,15 +437,14 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">version</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager">Second, install the vcfR package from Bioconductor using
-<code>BiocManager</code><a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a>
+<code>BiocManager</code>
 <a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a></h2>
 <hr class="half-width"><div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout">
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 </div>
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-</h3>
+<h3 class="callout-title">Head’s Up: Installing vcfR may take a while due to numerous dependencies</h3>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
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@@ -470,8 +466,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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-</h3>
+<h3 class="callout-title">Note: Installing packages from Bioconductor vs from CRAN</h3>
 <div class="callout-content">
 <p>Some packages begin by being available only on Bioconductor, and then
 later move to CRAN. <code>vcfR</code> is one such package, which
@@ -489,8 +484,7 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
-<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a></h2>
+</section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a></h2>
 <hr class="half-width"><p>While we are only focusing in this workshop on VCF analyses, there
 are hundreds or thousands of different types of data and analyses that
 bioinformaticians may want to work with. Sometimes you may get a new
@@ -502,8 +496,7 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website</h3>
 <div class="callout-content">
 <p>There are several thousand packages available through the
 Bioconductor website. It can be a bit of a challenge to find what you
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul><li>Use the <code>BiocManager::available()</code> function to see what
 packages are available matching a search term.</li>
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-</h3>
+<h3 class="callout-title">Tip: Refreshing the RStudio package view after installing</h3>
 <div class="callout-content">
 <p>If you install a package from Bioconductor, you may need to refresh
 the RStudio package view to see it in your list. You can do this by
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-</section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
+</section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
 <hr class="half-width"><ul><li><a href="https://bioconductor.org/" class="external-link">Bioconductor</a></li>
 <li><a href="https://bioconductor.org/packages/release/BiocViews.html#___Software" class="external-link">Bioconductor
 package search</a></li>
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 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Bioconductor is an alternative package repository for bioinformatics
 packages.</li>
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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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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -632,7 +621,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/04-bioconductor-vcfr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/05-dplyr.html b/instructor/05-dplyr.html
index bf1cd47e..4fff65ed 100644
--- a/instructor/05-dplyr.html
+++ b/instructor/05-dplyr.html
@@ -290,10 +290,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -439,8 +439,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-installing-packages" class="callout-inner">
-<h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
-</h3>
+<h3 class="callout-title">Tip: Installing packages</h3>
 <div class="callout-content">
 <p>It may be temping to install the <code>tidyverse</code> package, as
 it contains many useful collection of packages for this lesson and
@@ -452,8 +451,7 @@ <h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
-<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a></h2>
+<section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a></h2>
 <hr class="half-width"><p>The package <code>dplyr</code> is a fairly new (2014) package that
 tries to provide easy tools for the most common data manipulation tasks.
 This package is also included in the <a href="https://www.tidyverse.org/" class="external-link"><code>tidyverse</code> package</a>,
@@ -625,8 +623,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Create a table that contains all the columns with the letter “i” and
 column “POS”, without columns “Indiv” and “FILTER”. Hint: look at for a
@@ -680,7 +677,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<em> (continued)</em><a class="anchor" aria-label="anchor" href="#challenge"></a>
+<h3 class="callout-title">Challenge<em> (continued)</em>
 </h3>
 <div class="callout-content">
 <p>We can also get to <code>variants_result</code> in one line of
@@ -948,8 +945,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Select all the mutations that occurred between the positions 1e6 (one
 million) and 2e6 (inclusive) that have a QUAL greater than 200, and
@@ -1147,8 +1143,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-pipe-and-filter" class="callout-inner">
-<h3 class="callout-title">Exercise: Pipe and filter<a class="anchor" aria-label="anchor" href="#exercise-pipe-and-filter"></a>
-</h3>
+<h3 class="callout-title">Exercise: Pipe and filter</h3>
 <div class="callout-content">
 <p>Starting with the <code>variants</code> data frame, use pipes to
 subset the data to include only observations from SRR2584863 sample,
@@ -1239,8 +1234,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>There are a lot of columns in our data set, so let’s just look at the
 <code>sample_id</code>, <code>POS</code>, <code>QUAL</code>, and
@@ -1339,8 +1333,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul><li>How many mutations are INDELs?</li>
 </ul></div>
@@ -1423,8 +1416,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="grouped-data-frames-in-tidyverse" class="callout-inner">
-<h3 class="callout-title">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a>
-</h3>
+<h3 class="callout-title">Grouped Data Frames in Tidyverse</h3>
 <div class="callout-content">
 <p>When you group a data frame with <code>group_by()</code>, you get a
 grouped data frame. This is a special type of data frame that has all
@@ -1516,8 +1508,7 @@ <h3 id="resources">Resources<a class="anchor" aria-label="anchor" href="#resourc
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>Use the <code>dplyr</code> package to manipulate data frames.</li>
 <li>Use <code>glimpse()</code> to quickly look at your data frame.</li>
@@ -1575,7 +1566,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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 	<div id="to-top">
@@ -1598,7 +1589,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/05-dplyr.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
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   </script><script>
diff --git a/instructor/06-data-visualization.html b/instructor/06-data-visualization.html
index 328a971f..fcfce539 100644
--- a/instructor/06-data-visualization.html
+++ b/instructor/06-data-visualization.html
@@ -299,10 +299,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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                 </h2>
@@ -322,7 +322,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -402,7 +402,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong><a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
+<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong>
 <a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a></h2>
 <hr class="half-width"><figure><img src="https://ggplot2.tidyverse.org/logo.png" align="right" alt="Line plot enclosed in hexagon shape with ggplot2 typed beneath and www.rstudio.com at the bottom." class="figure mx-auto d-block"></figure><p><strong><code>ggplot2</code></strong> is a plotting package, part of
 the tidyverse, that makes it simple to create complex plots from data in
@@ -440,7 +440,7 @@ <h3 class="card-title">Objectives</h3>
 or discrete</a>, a quick way to check is to use the <a href="https://www.geeksforgeeks.org/get-summary-of-results-produced-by-functions-in-r-programming-summary-function/" class="external-link"><code>summary()</code></a>
 function. Continuous variables have descriptive statistics but not the
 discrete variables.</p>
-</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code><a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
+</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code>
 <a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a></h2>
 <hr class="half-width"><p>First, we need to install the <code>ggplot2</code> package.</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -488,8 +488,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <p>As we can see from above output <strong><code>ggplot2</code></strong>
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 <strong><code>tidyverse</code></strong> framework.</p>
-</section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a></h2>
+</section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a></h2>
 <hr class="half-width"><div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
@@ -850,8 +849,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="va">coverage_plot</span></span>
 <span>  <span class="op">+</span> <span class="fu">geom_point</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
-<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a></h2>
+</section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a></h2>
 <hr class="half-width"><p>Building plots with <strong><code>ggplot2</code></strong> is
 typically an iterative process. We start by defining the dataset we’ll
 use, lay out the axes, and choose a geom:</p>
@@ -943,8 +941,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of mapping quality
 (<code>MQ</code>) over position (<code>POS</code>) with the samples
@@ -958,7 +955,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -986,8 +983,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span>       title <span class="op">=</span> <span class="st">"Read Depth vs. Position"</span><span class="op">)</span> <span class="op">+</span></span>
 <span>  <span class="fu">theme</span><span class="op">(</span>text <span class="op">=</span> <span class="fu">element_text</span><span class="op">(</span>family <span class="op">=</span> <span class="st">"Bookman"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
 </div>
-<figure><img src="../fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a>
-<a class="anchor" aria-label="anchor" href="#faceting"></a></h2>
+<figure><img src="../fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a></h2>
 <hr class="half-width"><p><strong><code>ggplot2</code></strong> has a special technique called
 <em>faceting</em> that allows the user to split one plot into multiple
 plots (panels) based on a factor (variable) included in the dataset. We
@@ -1040,8 +1036,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of PHRED scaled
 quality (<code>QUAL</code>) over position (<code>POS</code>) with the
@@ -1055,7 +1050,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1071,8 +1066,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a>
-<a class="anchor" aria-label="anchor" href="#barplots"></a></h2>
+</section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a></h2>
 <hr class="half-width"><p>We can create barplots using the <a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link"><code>geom_bar</code></a>
 geom. Let’s make a barplot showing the number of variants for each
 sample that are indels.</p>
@@ -1089,8 +1083,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Since we already have the sample_id labels on the individual plot
 facets, we don’t need the legend. Use the help file for
@@ -1104,7 +1097,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1118,8 +1111,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a>
-<a class="anchor" aria-label="anchor" href="#density"></a></h2>
+</section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a></h2>
 <hr class="half-width"><p>We can create density plots using the <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 geom that shows the distribution of of a variable in the dataset. Let’s
 plot the distribution of <code>DP</code></p>
@@ -1137,8 +1129,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-3" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-3"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 to plot the distribution of <code>DP</code> with a different fill for
@@ -1151,7 +1142,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1166,8 +1157,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="ggplot2-themes">
-<strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
-<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a></h2>
+<strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a></h2>
 <hr class="half-width"><p>In addition to <a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link"><code>theme_bw()</code></a>,
 which changes the plot background to white,
 <strong><code>ggplot2</code></strong> comes with several other themes
@@ -1189,8 +1179,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="challenge-4" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-4"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>With all of this information in hand, please take another five
 minutes to either improve one of the plots generated in this exercise or
@@ -1204,8 +1193,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
-<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a></h2>
+</section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a></h2>
 <hr class="half-width"><p><strong><code>ggplot2</code></strong> offers many more informative
 and beautiful plots (<code>geoms</code>) of interest for biologists
 (although not covered in this lesson) that are worth exploring, such
@@ -1219,8 +1207,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <li>
 <a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link"><code>geom_violin()</code></a>,
 for violin plots</li>
-</ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
+</ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a></h2>
 <hr class="half-width"><ul><li>
 <a href="https://www.amazon.com/gp/product/331924275X/" class="external-link">ggplot2:
 Elegant Graphics for Data Analysis</a> (<a href="https://ggplot2-book.org/" class="external-link">online version</a>)</li>
@@ -1237,8 +1224,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>ggplot2 is a powerful tool for high-quality plots</li>
 <li>ggplot2 provides a flexible and readable grammar to build plots</li>
@@ -1281,7 +1267,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -1304,7 +1290,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/06-data-visualization.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/07-r-help.html b/instructor/07-r-help.html
index c3f74dd4..ca1c18a8 100644
--- a/instructor/07-r-help.html
+++ b/instructor/07-r-help.html
@@ -293,10 +293,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -316,7 +316,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -387,8 +387,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a></h2>
+<section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a></h2>
 <hr class="half-width"><figure><img src="../fig/oreilly_book_covers.png" alt="rstudio default session" style="width: 600px;" class="figure mx-auto d-block"></figure><p>No matter how much experience you have with R, you will find yourself
 needing help. There is no shame in researching how to do something in R,
 and most people will find themselves looking up how to do the same
@@ -397,8 +396,7 @@ <h3 class="card-title">Objectives</h3>
 <blockquote>
 <p>“Never memorize something that you can look up” -- A. Einstein</p>
 </blockquote>
-</section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
-<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a></h2>
+</section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a></h2>
 <hr class="half-width"><p>Two popular websites will be of great help with many R problems. For
 <strong>general</strong> <strong>R questions</strong>, <a href="https://stackoverflow.com/" class="external-link">Stack Overflow</a> is probably the
 most popular online community for developers. If you start your question
@@ -410,8 +408,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-asking-for-help-using-online-forums" class="callout-inner">
-<h3 class="callout-title">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
-</h3>
+<h3 class="callout-title">Tip: Asking for help using online forums:</h3>
 <div class="callout-content">
 <ul><li>When searching for R help, look for <a href="https://stackoverflow.com/questions/tagged/r" class="external-link">answers with the ‘r’
 tag</a>.</li>
@@ -427,8 +424,7 @@ <h3 class="callout-title">Tip: Asking for help using online forums:<a class="anc
 </ul></div>
 </div>
 </div>
-</section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
-<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a></h2>
+</section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a></h2>
 <hr class="half-width"><p>Often, in order to duplicate the issue you are having, someone may
 need to see the data you are working with or verify the versions of R or
 R packages you are using. The following R functions will help with
@@ -487,8 +483,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">saveRDS</span><span class="op">(</span><span class="va">iris</span>, file<span class="op">=</span><span class="st">"iris.rds"</span><span class="op">)</span> <span class="co"># By convention, we use the .rds file extension</span></span></code></pre>
 </div>
-</section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
-<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a></h2>
+</section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a></h2>
 <hr class="half-width"><p>Finally, here are a few pieces of introductory R knowledge that are
 too good to pass up. While we won’t return to them in this course, we
 put them here because they come up commonly:</p>
@@ -539,8 +534,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul><li>R provides thousands of functions for analyzing data, and provides
 several way to get help</li>
@@ -585,7 +579,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -608,7 +602,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/07-r-help.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 141c8c3c..9bf6b194 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -298,10 +298,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -322,7 +322,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="https://datacarpentry.github.io/genomics-r-intro/instructor/aio.html" class="external-link">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="https://datacarpentry.github.io/genomics-r-intro/instructor/aio.html" class="external-link">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -339,8 +339,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
     <main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Page not found</h1>
         
-<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
-<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
 <hr class="half-width"><p>We cannot seem to find the page you are looking for. Here are some
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 <ol style="list-style-type: decimal"><li>try going back to the <a href="javascript:history.back()">previous
@@ -375,7 +374,7 @@ <h1>Page not found</h1>
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-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/404.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
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+  "dateModified": "2024-08-27",
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diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index cf006fcc..76beba1b 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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                 </h2>
@@ -302,7 +302,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -392,7 +392,7 @@ <h1>Contributor Code of Conduct</h1>
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -415,7 +415,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
-  "datePublished": "2024-08-20"
+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 90cf9547..c26cfd89 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -302,7 +302,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -347,8 +347,7 @@ <h1>Licenses</h1>
 
         
 
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-<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
 Carpentry) instructional material is made available under the <a href="https://creativecommons.org/licenses/by/4.0/" class="external-link">Creative Commons
 Attribution license</a>. The following is a human-readable summary of
@@ -381,8 +380,7 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-<a class="anchor" aria-label="anchor" href="#software"></a></h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -402,8 +400,7 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
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-<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -443,7 +440,7 @@ <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>
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 			</div>
 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -466,7 +463,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/LICENSE.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
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+  "datePublished": "2024-08-27"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index bee15658..4ebaec15 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -343,10 +343,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
             </div>
 
             <hr class="half-width">
-<div class="accordion accordion-flush resources" id="accordionFlush12">
+<div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
                   </button>
                 </h2>
@@ -370,7 +370,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources">
+            <hr class="half-width lesson-resources">
 <a href="../instructor/aio.html">See all in one page</a>
 
 
@@ -442,7 +442,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="getting-ready-to-use-r-for-the-first-time">Getting ready to use R for the first time<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
-<a class="anchor" aria-label="anchor" href="#getting-ready-to-use-r-for-the-first-time"></a>
 </h2>
 <hr class="half-width">
 <p>In this lesson we will take you through the very first things you
@@ -452,8 +451,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-this-lesson-works-best-on-the-cloud" class="callout-inner">
-<h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anchor" aria-label="anchor" href="#tip-this-lesson-works-best-on-the-cloud"></a>
-</h3>
+<h3 class="callout-title">Tip: This lesson works best on the cloud</h3>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
 virtual machine instances provided to you at a genomics workshop. Much
@@ -466,7 +464,6 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 </div>
 </div>
 </section><section><h2 class="section-heading" id="a-brief-history-of-r">A Brief History of R<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
-<a class="anchor" aria-label="anchor" href="#a-brief-history-of-r"></a>
 </h2>
 <hr class="half-width">
 <p><a href="https://en.wikipedia.org/wiki/R_(programming_language)" class="external-link">The
@@ -476,7 +473,6 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 Labs and was developed to teach intro statistics. See this <a href="https://www.stat.auckland.ac.nz/~ihaka/downloads/Massey.pdf" class="external-link">slide
 deck</a> by Ross Ihaka for more info on the subject.</p>
 </section><section><h2 class="section-heading" id="advantages-of-using-r">Advantages of using R<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
-<a class="anchor" aria-label="anchor" href="#advantages-of-using-r"></a>
 </h2>
 <hr class="half-width">
 <p>At more than 20 years old, R is fairly mature and <a href="https://www.tiobe.com/tiobe-index/r/" class="external-link">growing in popularity</a>.
@@ -510,8 +506,7 @@ <h3 class="callout-title">Tip: This lesson works best on the cloud<a class="anch
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="discussion-your-experience" class="callout-inner">
-<h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-label="anchor" href="#discussion-your-experience"></a>
-</h3>
+<h3 class="callout-title">Discussion: Your experience</h3>
 <div class="callout-content">
 <p>What has motivated you to learn R? Have you had a research question
 for which spreadsheet programs such as Excel have proven difficult to
@@ -520,7 +515,6 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 </div>
 </div>
 </section><section><h2 class="section-heading" id="introducing-rstudio-server">Introducing RStudio Server<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-rstudio-server"></a>
 </h2>
 <hr class="half-width">
 <p>In these lessons, we will be making use of a software called <a href="https://www.rstudio.com/products/RStudio/" class="external-link">RStudio</a>, an <a href="https://en.wikipedia.org/wiki/Integrated_development_environment" class="external-link">Integrated
@@ -533,7 +527,6 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 browser. RStudio Server has the same features of the Desktop version of
 RStudio you could download as standalone software.</p>
 </section><section><h2 class="section-heading" id="log-on-to-rstudio-server">Log on to RStudio Server<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
-<a class="anchor" aria-label="anchor" href="#log-on-to-rstudio-server"></a>
 </h2>
 <hr class="half-width">
 <p>Open a web browser and enter the URL you used to log in at the
@@ -546,8 +539,7 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout-inner">
-<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.<a class="anchor" aria-label="anchor" href="#tip-make-sure-there-are-no-spaces-before-or-after-your-url."></a>
-</h3>
+<h3 class="callout-title">Tip: Make sure there are no spaces before or after your URL.</h3>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -561,7 +553,6 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or after you
 by your instructors.</p>
 <p>You should now see the RStudio interface:</p>
 <figure><img src="../fig/rstudio_session_default.png" alt="rstudio default session" style="width:1000px;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="create-an-rstudio-project">Create an RStudio project<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
-<a class="anchor" aria-label="anchor" href="#create-an-rstudio-project"></a>
 </h2>
 <hr class="half-width">
 <p>One of the first benefits we will take advantage of in RStudio is
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 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-make-your-project-more-reproducible-with-renv" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Tip: Make your project more reproducible with renv</h3>
 <div class="callout-content">
 <p>One of the most wonderful and also frustrating aspects of working
 with R is managing packages. We will talk more about them, but packages
@@ -629,7 +619,6 @@ <h3 class="callout-title">Tip: Make your project more reproducible with renv<a c
 </div>
 </div>
 </section><section><h2 class="section-heading" id="creating-your-first-r-script">Creating your first R script<a class="anchor" aria-label="anchor" href="#creating-your-first-r-script"></a>
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 </h2>
 <hr class="half-width">
 <p>Now that we are ready to start exploring R, we will want to keep a
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 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-save-your-script-now" class="callout-inner">
-<h3 class="callout-title">Tip: Save your script now<a class="anchor" aria-label="anchor" href="#tip-save-your-script-now"></a>
-</h3>
+<h3 class="callout-title">Tip: Save your script now</h3>
 <div class="callout-content">
 <p>Remember to save your script at this point. Anything can happen
 during your lesson and you don’t want to lose your work!</p>
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 </div>
 </div>
 </section><section><h2 class="section-heading" id="overview-and-customization-of-the-rstudio-layout">Overview and customization of the RStudio layout<a class="anchor" aria-label="anchor" href="#overview-and-customization-of-the-rstudio-layout"></a>
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 </h2>
 <hr class="half-width">
 <p>Here are the major windows (or panes) of the RStudio environment:</p>
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 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-uploads-and-downloads-in-the-cloud" class="callout-inner">
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 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
 cloud instance (click the “more” button) to your local computer. Uploads
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 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="you-are-working-with-r" class="callout-inner">
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-</h3>
+<h3 class="callout-title">You are working with R</h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
 of reasons to. For example, once you have written an RScript, you can
@@ -732,7 +717,6 @@ <h3 class="callout-title">You are working with R<a class="anchor" aria-label="an
 </div>
 </div>
 </section><section><h2 class="section-heading" id="getting-to-work-with-r-navigating-directories">Getting to work with R: navigating directories<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
-<a class="anchor" aria-label="anchor" href="#getting-to-work-with-r-navigating-directories"></a>
 </h2>
 <hr class="half-width">
 <p>Now that we have covered the more aesthetic aspects of RStudio, we
@@ -776,8 +760,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-work-interactively-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" aria-label="anchor" href="#exercise-work-interactively-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Work interactively in R</h3>
 <div class="callout-content">
 <p>What happens when you try to enter the <code>getwd()</code> command
 in the Console pane?</p>
@@ -836,7 +819,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-never-use-setwd" class="callout-inner">
-<h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
+<h3 class="callout-title">Tip: Never use <code>setwd()</code>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -854,7 +837,6 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 </div>
 </div>
 </section><section><h2 class="section-heading" id="using-functions-in-r-without-needing-to-master-them">Using functions in R, without needing to master them<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
-<a class="anchor" aria-label="anchor" href="#using-functions-in-r-without-needing-to-master-them"></a>
 </h2>
 <hr class="half-width">
 <p>A function in R (or any computing language) is a short program that
@@ -867,8 +849,7 @@ <h3 class="callout-title">Tip: Never use <code>setwd()</code><a class="anchor" a
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-what-do-these-functions-do" class="callout-inner">
-<h3 class="callout-title">Exercise: What do these functions do?<a class="anchor" aria-label="anchor" href="#exercise-what-do-these-functions-do"></a>
-</h3>
+<h3 class="callout-title">Exercise: What do these functions do?</h3>
 <div class="callout-content">
 <p>Try the following functions by writing them in your script. See if
 you can guess what they do, and make sure to add comments to your script
@@ -930,7 +911,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] 3</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="getting-help-with-function-arguments">Getting help with function arguments<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-function-arguments"></a>
 </h2>
 <hr class="half-width">
 <p>What if you wanted to round to one significant digit?
@@ -1021,8 +1001,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-searching-for-r-functions" class="callout-inner">
-<h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" aria-label="anchor" href="#exercise-searching-for-r-functions"></a>
-</h3>
+<h3 class="callout-title">Exercise: Searching for R functions</h3>
 <div class="callout-content">
 <p>Use <code>help.search()</code> to find R functions for the following
 statistical functions. Remember to put your search query in quotes
@@ -1064,7 +1043,6 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 main repository for R, and <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> - a popular repository
 for bioinformatics-related R packages.</p>
 </section><section><h2 class="section-heading" id="rstudio-contextual-help">RStudio contextual help<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
-<a class="anchor" aria-label="anchor" href="#rstudio-contextual-help"></a>
 </h2>
 <hr class="half-width">
 <p>Here is one last bonus we will mention about RStudio. It’s difficult
@@ -1080,8 +1058,7 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>R is a powerful, popular open-source scripting language</li>
@@ -1137,7 +1114,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 <section><h2 class="section-heading" id="the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r">“The fantastic world of R awaits you” OR “Nobody wants to learn how
 to use R”<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
-<a class="anchor" aria-label="anchor" href="#the-fantastic-world-of-r-awaits-you-or-nobody-wants-to-learn-how-to-use-r"></a>
 </h2>
 <hr class="half-width">
 <p>Before we begin this lesson, we want you to be clear on the goal of
@@ -1153,7 +1129,6 @@ <h3 class="card-title">Objectives</h3>
 less frustration, and in less time - the fantastic world of R awaits
 you!</p>
 </section><section><h2 class="section-heading" id="what-these-lessons-will-not-teach-you">What these lessons will not teach you<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
-<a class="anchor" aria-label="anchor" href="#what-these-lessons-will-not-teach-you"></a>
 </h2>
 <hr class="half-width">
 <p>Nobody wants to learn how to use R. People want to learn how to use R
@@ -1183,8 +1158,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-where-to-learn-more" class="callout-inner">
-<h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
-</h3>
+<h3 class="callout-title">Tip: Where to learn more</h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
 them can be quite technical, but if you are a regular R user you may
@@ -1217,7 +1191,6 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="creating-objects-in-r">Creating objects in R<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#creating-objects-in-r"></a>
 </h2>
 <hr class="half-width">
 <div id="reminder" class="callout prereq">
@@ -1225,8 +1198,7 @@ <h3 class="callout-title">Tip: Where to learn more<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="check"></i>
 </div>
 <div id="reminder" class="callout-inner">
-<h3 class="callout-title">Reminder<a class="anchor" aria-label="anchor" href="#reminder"></a>
-</h3>
+<h3 class="callout-title">Reminder</h3>
 <div class="callout-content">
 <p>At this point you should be coding along in the
 “<strong>genomics_r_basics.R</strong>” script we created in the last
@@ -1299,8 +1271,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-some-objects-in-r" class="callout-inner">
-<h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" aria-label="anchor" href="#exercise-create-some-objects-in-r"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create some objects in R</h3>
 <div class="callout-content">
 <p>Create the following objects; give each object an appropriate name
 (your best guess at what name to use is fine):</p>
@@ -1337,7 +1308,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </div>
 </section><section><h2 class="section-heading" id="naming-objects-in-r">Naming objects in R<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
-<a class="anchor" aria-label="anchor" href="#naming-objects-in-r"></a>
 </h2>
 <hr class="half-width">
 <p>Here are some important details about naming objects in R.</p>
@@ -1386,8 +1356,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout-inner">
-<h3 class="callout-title">Tip: Pay attention to warnings in the script console<a class="anchor" aria-label="anchor" href="#tip-pay-attention-to-warnings-in-the-script-console"></a>
-</h3>
+<h3 class="callout-title">Tip: Pay attention to warnings in the script console</h3>
 <div class="callout-content">
 <p>If you enter a line of code in your script that contains an error,
 RStudio may give you an error message and underline this mistake.
@@ -1402,7 +1371,6 @@ <h3 class="callout-title">Tip: Pay attention to warnings in the script console<a
 </div>
 </div>
 </section><section><h2 class="section-heading" id="reassigning-object-names-or-deleting-objects">Reassigning object names or deleting objects<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
-<a class="anchor" aria-label="anchor" href="#reassigning-object-names-or-deleting-objects"></a>
 </h2>
 <hr class="half-width">
 <p>Once an object has a value, you can change that value by overwriting
@@ -1435,7 +1403,6 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <pre class="error" tabindex="0"><code>Error: object 'gene_name' not found</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="understanding-object-data-types-classes-and-modes">Understanding object data types (classes and modes)<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
-<a class="anchor" aria-label="anchor" href="#understanding-object-data-types-classes-and-modes"></a>
 </h2>
 <hr class="half-width">
 <p>In R, <strong>every object has several properties</strong>:</p>
@@ -1459,8 +1426,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-classess-vs.-modes" class="callout-inner">
-<h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="anchor" href="#tip-classess-vs.-modes"></a>
-</h3>
+<h3 class="callout-title">Tip: Classess vs. modes</h3>
 <div class="callout-content">
 <p>The difference between modes and classes is a bit
 <strong>confusing</strong> and the subject of several <a href="https://stackoverflow.com/questions/35445112/what-is-the-difference-between-mode-and-class-in-r" class="external-link">online
@@ -1525,8 +1491,7 @@ <h3 class="callout-title">Tip: Classess vs. modes<a class="anchor" aria-label="
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-modes" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their modes<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-modes"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their modes</h3>
 <div class="callout-content">
 <p>Create the following objects in R, then use the <code>mode()</code>
 function to verify their modes. Try to guess what the mode will be
@@ -1612,8 +1577,7 @@ <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-create-objects-and-check-their-class-using-class" class="callout-inner">
-<h3 class="callout-title">Exercise: Create objects and check their class using “class”<a class="anchor" aria-label="anchor" href="#exercise-create-objects-and-check-their-class-using-class"></a>
-</h3>
+<h3 class="callout-title">Exercise: Create objects and check their class using “class”</h3>
 <div class="callout-content">
 <p>Using the objects created in the previous challenge, use the
 <code>class()</code> function to check their classes.</p>
@@ -1724,7 +1688,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="mathematical-and-functional-operations-on-objects">Mathematical and functional operations on objects<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
-<a class="anchor" aria-label="anchor" href="#mathematical-and-functional-operations-on-objects"></a>
 </h2>
 <hr class="half-width">
 <p>Once an object exists (which by definition also means it has a mode),
@@ -1803,8 +1766,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-compute-the-golden-ratio" class="callout-inner">
-<h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" aria-label="anchor" href="#exercise-compute-the-golden-ratio"></a>
-</h3>
+<h3 class="callout-title">Exercise: Compute the golden ratio</h3>
 <div class="callout-content">
 <p>One approximation of the golden ratio (φ) can be found by taking the
 sum of 1 and the square root of 5, and dividing by 2 as in the example
@@ -1838,7 +1800,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="vectors">Vectors<a class="anchor" aria-label="anchor" href="#vectors"></a>
-<a class="anchor" aria-label="anchor" href="#vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Vectors are probably the most used commonly used object type in R.
@@ -1900,7 +1861,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 we learn here about vectors will pay off even more when we start working
 with data frames.</p>
 </section><section><h2 class="section-heading" id="creating-and-subsetting-vectors">Creating and subsetting vectors<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#creating-and-subsetting-vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Let’s create a few more vectors to play around with:</p>
@@ -1982,7 +1942,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "rs53576"   "rs1815739" "rs6152"    "rs1799971"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="adding-to-removing-or-replacing-values-in-existing-vectors">Adding to, removing, or replacing values in existing vectors<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
-<a class="anchor" aria-label="anchor" href="#adding-to-removing-or-replacing-values-in-existing-vectors"></a>
 </h2>
 <hr class="half-width">
 <p>Once you have an existing vector, you may want to add a new item to
@@ -2054,8 +2013,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-examining-and-subsetting-vectors" class="callout-inner">
-<h3 class="callout-title">Exercise: Examining and subsetting vectors<a class="anchor" aria-label="anchor" href="#exercise-examining-and-subsetting-vectors"></a>
-</h3>
+<h3 class="callout-title">Exercise: Examining and subsetting vectors</h3>
 <div class="callout-content">
 <p>Answer the following questions to test your knowledge of vectors</p>
 <p>Which of the following are true of vectors in R? A) All vectors have
@@ -2096,7 +2054,6 @@ <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </div>
 </div>
 </section><section><h2 class="section-heading" id="logical-subsetting">Logical Subsetting<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
-<a class="anchor" aria-label="anchor" href="#logical-subsetting"></a>
 </h2>
 <hr class="half-width">
 <p>There is one last set of cool subsetting capabilities we want to
@@ -2172,8 +2129,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="the-magic-of-programming" class="callout-inner">
-<h3 class="callout-title">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
-</h3>
+<h3 class="callout-title">The magic of programming</h3>
 <div class="callout-content">
 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
@@ -2251,7 +2207,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="a-few-final-vector-tricks">A few final vector tricks<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
-<a class="anchor" aria-label="anchor" href="#a-few-final-vector-tricks"></a>
 </h2>
 <hr class="half-width">
 <p>Finally, there are a few other common retrieve or replace operations
@@ -2301,8 +2256,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <div id="tip-whats-the-difference-between-the-in-and-the-operators" class="callout-inner">
 <h3 class="callout-title">Tip: What’s the difference between the
-<code>%in% and the</code>==` operators?<a class="anchor" aria-label="anchor" href="#tip-whats-the-difference-between-the-in-and-the-operators"></a>
-</h3>
+<code>%in% and the</code>==` operators?</h3>
 <div class="callout-content">
 <p>The <code>%in%</code> operator is used to test if the elements of a
 vector are present in another vector. In the example above, if both
@@ -2329,8 +2283,7 @@ <h3 class="callout-title">Tip: What’s the difference between the
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-1" class="callout-inner">
-<h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor" href="#review-exercise-1"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 1</h3>
 <div class="callout-content">
 <p>What data modes are the following vectors? a. <code>snps</code><br>
 b. <code>snp_chromosomes</code><br>
@@ -2387,8 +2340,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-2" class="callout-inner">
-<h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor" href="#review-exercise-2"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 2</h3>
 <div class="callout-content">
 <p>Add the following values to the specified vectors: a. To the
 <code>snps</code> vector add: “rs662799”<br>
@@ -2449,8 +2401,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-3" class="callout-inner">
-<h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor" href="#review-exercise-3"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 3</h3>
 <div class="callout-content">
 <p>Make the following change to the <code>snp_genes</code> vector:</p>
 <p>Hint: Your vector should look like this in ‘Environment’:
@@ -2496,8 +2447,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-4" class="callout-inner">
-<h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor" href="#review-exercise-4"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 4</h3>
 <div class="callout-content">
 <p>Using indexing, create a new vector named <code>combined</code> that
 contains:</p>
@@ -2542,8 +2492,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="review-exercise-5" class="callout-inner">
-<h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor" href="#review-exercise-5"></a>
-</h3>
+<h3 class="callout-title">Review Exercise 5</h3>
 <div class="callout-content">
 <p>What type of data is <code>combined</code>?</p>
 </div>
@@ -2576,8 +2525,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="lists" class="callout-inner">
-<h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
-</h3>
+<h3 class="callout-title">Lists</h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
 genomics lessons. That said, you may come across lists in the way that
@@ -2652,8 +2600,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Effectively using R is a journey of months or years. Still you don’t
@@ -2705,7 +2652,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="preface">Preface<a class="anchor" aria-label="anchor" href="#preface"></a>
-<a class="anchor" aria-label="anchor" href="#preface"></a>
 </h2>
 <hr class="half-width">
 <p>The Intro to R and RStudio for Genomics is a part of the Genomics
@@ -2725,7 +2671,6 @@ <h3 class="card-title">Objectives</h3>
 </li>
 <li>Dataset publicly available - in this case through the NCBI SRA (<a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">http://www.ncbi.nlm.nih.gov/sra</a>)</li>
 </ul></section><section><h2 class="section-heading" id="introduction-to-the-dataset">Introduction to the dataset<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#introduction-to-the-dataset"></a>
 </h2>
 <hr class="half-width">
 <p>Microbes are ideal organisms for exploring ‘Long-term Evolution
@@ -2810,7 +2755,6 @@ <h3 class="card-title">Objectives</h3>
 strains?</li>
 <li>What are the base pair changes between strains?</li>
 </ul></section><section><h2 class="section-heading" id="how-vcf-files-are-generated">How VCF files are generated<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
-<a class="anchor" aria-label="anchor" href="#how-vcf-files-are-generated"></a>
 </h2>
 <hr class="half-width">
 <p>Publicly accessible sequencing files in FASTQ formats can be
@@ -2824,7 +2768,6 @@ <h3 class="card-title">Objectives</h3>
 <img src="../fig/variant_calling_workflow.png" alt="variant calling workflow. Sequence reads (FASTQ files), Quality control (FASTQ files), Alignment to Genome (SAM/BAM files), Alignment cleanup (BAM file ready for variant calling), Variant Calling (VCF file)" style="width: 250px;" class="figure">
 </center>
 </section><section><h2 class="section-heading" id="how-variant-calls-are-stored-in-vcf-files">How variant calls are stored in VCF files<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
-<a class="anchor" aria-label="anchor" href="#how-variant-calls-are-stored-in-vcf-files"></a>
 </h2>
 <hr class="half-width">
 <p>VCF files contain variants that were called against a reference
@@ -2981,7 +2924,6 @@ <h3 class="card-title">Objectives</h3>
 <p>For more information on VCF files visit The Broad Institute’s <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format" class="external-link">VCF
 guide</a>.</p>
 </section><section><h2 class="section-heading" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
-<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <hr class="half-width">
 <p>Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL,
@@ -3003,8 +2945,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>The dataset comes from a real world experiment in E. coli.</li>
@@ -3069,7 +3010,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="working-with-spreadsheets-tabular-data">Working with spreadsheets (tabular data)<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
-<a class="anchor" aria-label="anchor" href="#working-with-spreadsheets-tabular-data"></a>
 </h2>
 <hr class="half-width">
 <p>A substantial amount of the data we work with in genomics will be
@@ -3107,8 +3047,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-keep-your-raw-data-separate" class="callout-inner">
-<h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
-</h3>
+<h3 class="callout-title">Tip: Keep your raw data separate</h3>
 <div class="callout-content">
 <p>When you work with data in R, you are not changing the original file
 you loaded that data from. This is different than (for example) working
@@ -3121,7 +3060,6 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 </div>
 </section><section><h2 class="section-heading" id="importing-tabular-data-into-r">Importing tabular data into R<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
-<a class="anchor" aria-label="anchor" href="#importing-tabular-data-into-r"></a>
 </h2>
 <hr class="half-width">
 <p>There are several ways to import data into R. For our purpose here,
@@ -3135,8 +3073,7 @@ <h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria
 </div>
 <div id="exercise-review-the-arguments-of-the-read.csv-function" class="callout-inner">
 <h3 class="callout-title">Exercise: Review the arguments of the
-<code>read.csv()</code> function<a class="anchor" aria-label="anchor" href="#exercise-review-the-arguments-of-the-read.csv-function"></a>
-</h3>
+<code>read.csv()</code> function</h3>
 <div class="callout-content">
 <p><strong>Before using the <code>read.csv()</code> function, use R’s
 help feature to answer the following questions</strong>.</p>
@@ -3163,7 +3100,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li><p>The <code>read.csv()</code> function has the argument ‘header’
@@ -3192,8 +3129,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
-<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
-</h3>
+<h3 class="callout-title">Tip: Why does ?read.csv open the documentations to read.table?</h3>
 <div class="callout-content">
 <p>The reason for this is because <code>read.csv</code> is actually a
 short cut for <code>read.table("file.csv", sep = ",")</code>. You can
@@ -3233,8 +3169,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 name of the object will open a view of the data in a new tab.</p>
 <figure><img src="../%22fig/rstudio_dataframeview.png%22" alt="RStudio data frame view" class="figure mx-auto d-block"><div class="figcaption">RStudio data frame view</div>
 </figure></section><section><h2 class="section-heading" id="summarizing-subsetting-and-determining-the-structure-of-a-data-frame-">Summarizing, subsetting, and determining the structure of a data
-frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame."></a>
-<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a>
+frame.<a class="anchor" aria-label="anchor" href="#summarizing-subsetting-and-determining-the-structure-of-a-data-frame-"></a>
 </h2>
 <hr class="half-width">
 <p>A <strong>data frame is the standard way in R to store tabular
@@ -3363,8 +3298,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Exercise: Revisiting modes and classess<a class="anchor" aria-label="anchor" href="#challenge2"></a>
-</h3>
+<h3 class="callout-title">Exercise: Revisiting modes and classess</h3>
 <div class="callout-content">
 <p>Remeber when we said mode and class are sometimes different? If you
 do, here is a chance to check. What happens when you try the
@@ -3381,7 +3315,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3418,7 +3352,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </li>
 </ul></section><section><h2 class="section-heading" id="introducing-factors">Introducing Factors<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
-<a class="anchor" aria-label="anchor" href="#introducing-factors"></a>
 </h2>
 <hr class="half-width">
 <p>Factors are the final major data structure we will introduce in our R
@@ -3552,8 +3485,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
-<h3 class="callout-title">Tip: treating objects as categories without changing their mode<a class="anchor" aria-label="anchor" href="#tip-treating-objects-as-categories-without-changing-their-mode"></a>
-</h3>
+<h3 class="callout-title">Tip: treating objects as categories without changing their mode</h3>
 <div class="callout-content">
 <p>You don’t have to make an object a factor to get the benefits of
 treating an object as a factor. See what happens when you use the
@@ -3565,7 +3497,6 @@ <h3 class="callout-title">Tip: treating objects as categories without changing t
 </div>
 </div>
 </section><section><h2 class="section-heading" id="plotting-and-ordering-factors">Plotting and ordering factors<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
-<a class="anchor" aria-label="anchor" href="#plotting-and-ordering-factors"></a>
 </h2>
 <hr class="half-width">
 <p>One of the most common uses for factors will be when you plot
@@ -3624,8 +3555,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout-inner">
-<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?<a class="anchor" aria-label="anchor" href="#tip-packages-in-r-what-are-they-and-why-do-we-use-them"></a>
-</h3>
+<h3 class="callout-title">Tip: Packages in R – what are they and why do we use them?</h3>
 <div class="callout-content">
 <p>Packages are simply collections of functions and/or data that can be
 used to extend the capabilities of R beyond the core functionality that
@@ -3660,7 +3590,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </section><section><h2 class="section-heading" id="subsetting-data-frames">Subsetting data frames<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#subsetting-data-frames"></a>
 </h2>
 <hr class="half-width">
 <p>Next, we are going to talk about how you can get specific values from
@@ -3676,8 +3605,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-subsetting-a-data-frame" class="callout-inner">
-<h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" aria-label="anchor" href="#exercise-subsetting-a-data-frame"></a>
-</h3>
+<h3 class="callout-title">Exercise: Subsetting a data frame</h3>
 <div class="callout-content">
 <p><strong>Try the following indices and functions and try to figure out
 what they return</strong></p>
@@ -3703,7 +3631,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol>
@@ -4113,7 +4041,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
                                                                      </code></pre>
 </div>
 </section><section><h2 class="section-heading" id="coercing-values-in-data-frames">Coercing values in data frames<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
-<a class="anchor" aria-label="anchor" href="#coercing-values-in-data-frames"></a>
 </h2>
 <hr class="half-width">
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout">
@@ -4121,8 +4048,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>While we are going to address coercion in the context of data frames
 most of these methods apply to other data structures, such as
@@ -4317,7 +4243,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <pre class="output" tabindex="0"><code>[1] "character"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="stringsasfactors">StringsAsFactors = ?<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
-<a class="anchor" aria-label="anchor" href="#stringsasfactors"></a>
 </h2>
 <hr class="half-width">
 <p>Lets summarize this section on coercion with a few take home
@@ -4339,8 +4264,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames-1"></a>
-</h3>
+<h3 class="callout-title">Tip: coercion isn’t limited to data frames</h3>
 <div class="callout-content">
 <p>Prior to R 4.0 when importing a data frame using any one of the
 <code>read.table()</code> functions such as <code>read.csv()</code> ,
@@ -4355,7 +4279,6 @@ <h3 class="callout-title">Tip: coercion isn’t limited to data frames<a class="
 </div>
 </div>
 </section><section><h2 class="section-heading" id="data-frame-bonus-material-math-sorting-renaming">Data frame bonus material: math, sorting, renaming<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
-<a class="anchor" aria-label="anchor" href="#data-frame-bonus-material-math-sorting-renaming"></a>
 </h2>
 <hr class="half-width">
 <p>Here are a few operations that don’t need much explanation, but which
@@ -4401,8 +4324,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>The <code>order()</code> function lists values in increasing order by
 default. Look at the documentation for this function and change
@@ -4416,7 +4338,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4457,7 +4379,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 [29] "gt_GT_alleles"</code></pre>
 </div>
 </section><section><h2 class="section-heading" id="saving-your-data-frame-to-a-file">Saving your data frame to a file<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
-<a class="anchor" aria-label="anchor" href="#saving-your-data-frame-to-a-file"></a>
 </h2>
 <hr class="half-width">
 <p>We can save data to a file. We will save our
@@ -4475,7 +4396,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 provide a file name, the file will be written in the current working
 directory).</p>
 </section><section><h2 class="section-heading" id="importing-data-from-excel">Importing data from Excel<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
-<a class="anchor" aria-label="anchor" href="#importing-data-from-excel"></a>
 </h2>
 <hr class="half-width">
 <p>Excel is one of the most common formats, so we need to discuss how to
@@ -4540,8 +4460,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="exercise-putting-it-all-together---data-frames" class="callout-inner">
-<h3 class="callout-title">Exercise: Putting it all together - data frames<a class="anchor" aria-label="anchor" href="#exercise-putting-it-all-together---data-frames"></a>
-</h3>
+<h3 class="callout-title">Exercise: Putting it all together - data frames</h3>
 <div class="callout-content">
 <p><strong>Using the <code>Ecoli_metadata</code> data frame created
 above, answer the following questions</strong></p>
@@ -4571,7 +4490,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data frames<a clas
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb91">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4650,8 +4569,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>It is easy to import data into R from tabular formats including
@@ -4705,7 +4623,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="installing-packages-from-somewhere-else-besides-cran">Installing packages from somewhere else besides CRAN?<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
-<a class="anchor" aria-label="anchor" href="#installing-packages-from-somewhere-else-besides-cran"></a>
 </h2>
 <hr class="half-width">
 <p>So far we have told you about using packages that are included in the
@@ -4723,7 +4640,6 @@ <h3 class="card-title">Objectives</h3>
 analysis of biological data, and that it can be a great place to look
 for tools to help you analyze your -omics datasets!</p>
 </section><section><h2 class="section-heading" id="so-how-do-i-use-it">So how do I use it?<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
-<a class="anchor" aria-label="anchor" href="#so-how-do-i-use-it"></a>
 </h2>
 <hr class="half-width">
 <p>Since access to the <a href="https://bioconductor.org/" class="external-link">Bioconductor</a> repository is not
@@ -4733,7 +4649,6 @@ <h3 class="card-title">Objectives</h3>
 are working on, but you can use the same approach to install any of the
 many thousands of available packages.</p>
 <figure><img src="../fig/bioconductor_website_screenshot.jpg" alt="screenshot of bioconductor homepage" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="first-install-the-biocmanager-package">First, install the <code>BiocManager</code> package<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
-<a class="anchor" aria-label="anchor" href="#first-install-the-biocmanager-package"></a>
 </h2>
 <hr class="half-width">
 <p>The first step is to install a package that <em>is</em> on CRAN,
@@ -4761,7 +4676,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">version</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager">Second, install the vcfR package from Bioconductor using
-<code>BiocManager</code><a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a>
+<code>BiocManager</code>
 <a class="anchor" aria-label="anchor" href="#second-install-the-vcfr-package-from-bioconductor-using-biocmanager"></a>
 </h2>
 <hr class="half-width">
@@ -4770,8 +4685,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout-inner">
-<h3 class="callout-title">Head’s Up: Installing vcfR may take a while due to numerous dependencies<a class="anchor" aria-label="anchor" href="#heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies"></a>
-</h3>
+<h3 class="callout-title">Head’s Up: Installing vcfR may take a while due to numerous dependencies</h3>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
 can take a while.</p>
@@ -4793,8 +4707,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout-inner">
-<h3 class="callout-title">Note: Installing packages from Bioconductor vs from CRAN<a class="anchor" aria-label="anchor" href="#note-installing-packages-from-bioconductor-vs-from-cran"></a>
-</h3>
+<h3 class="callout-title">Note: Installing packages from Bioconductor vs from CRAN</h3>
 <div class="callout-content">
 <p>Some packages begin by being available only on Bioconductor, and then
 later move to CRAN. <code>vcfR</code> is one such package, which
@@ -4813,7 +4726,6 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 </div>
 </div>
 </section><section><h2 class="section-heading" id="search-for-bioconductor-packages-based-on-your-analysis-needs">Search for Bioconductor packages based on your analysis needs<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
-<a class="anchor" aria-label="anchor" href="#search-for-bioconductor-packages-based-on-your-analysis-needs"></a>
 </h2>
 <hr class="half-width">
 <p>While we are only focusing in this workshop on VCF analyses, there
@@ -4827,8 +4739,7 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs from CR
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout-inner">
-<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website<a class="anchor" aria-label="anchor" href="#tip-searching-for-packages-on-the-bioconductor-website"></a>
-</h3>
+<h3 class="callout-title">Tip: Searching for packages on the Bioconductor website</h3>
 <div class="callout-content">
 <p>There are several thousand packages available through the
 Bioconductor website. It can be a bit of a challenge to find what you
@@ -4847,8 +4758,7 @@ <h3 class="callout-title">Tip: Searching for packages on the Bioconductor websit
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul>
 <li>Use the <code>BiocManager::available()</code> function to see what
@@ -4867,8 +4777,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-refreshing-the-rstudio-package-view-after-installing" class="callout-inner">
-<h3 class="callout-title">Tip: Refreshing the RStudio package view after installing<a class="anchor" aria-label="anchor" href="#tip-refreshing-the-rstudio-package-view-after-installing"></a>
-</h3>
+<h3 class="callout-title">Tip: Refreshing the RStudio package view after installing</h3>
 <div class="callout-content">
 <p>If you install a package from Bioconductor, you may need to refresh
 the RStudio package view to see it in your list. You can do this by
@@ -4877,7 +4786,6 @@ <h3 class="callout-title">Tip: Refreshing the RStudio package view after install
 </div>
 </div>
 </section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
@@ -4891,8 +4799,7 @@ <h3 class="callout-title">Tip: Refreshing the RStudio package view after install
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Bioconductor is an alternative package repository for bioinformatics
@@ -5002,8 +4909,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-installing-packages" class="callout-inner">
-<h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
-</h3>
+<h3 class="callout-title">Tip: Installing packages</h3>
 <div class="callout-content">
 <p>It may be temping to install the <code>tidyverse</code> package, as
 it contains many useful collection of packages for this lesson and
@@ -5016,7 +4922,6 @@ <h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="
 </div>
 </div>
 <section><h2 class="section-heading" id="what-is-dplyr">What is dplyr?<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
-<a class="anchor" aria-label="anchor" href="#what-is-dplyr"></a>
 </h2>
 <hr class="half-width">
 <p>The package <code>dplyr</code> is a fairly new (2014) package that
@@ -5193,8 +5098,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Create a table that contains all the columns with the letter “i” and
 column “POS”, without columns “Indiv” and “FILTER”. Hint: look at for a
@@ -5248,7 +5152,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<em> (continued)</em><a class="anchor" aria-label="anchor" href="#challenge"></a>
+<h3 class="callout-title">Challenge<em> (continued)</em>
 </h3>
 <div class="callout-content">
 <p>We can also get to <code>variants_result</code> in one line of
@@ -5516,8 +5420,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Select all the mutations that occurred between the positions 1e6 (one
 million) and 2e6 (inclusive) that have a QUAL greater than 200, and
@@ -5716,8 +5619,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="exercise-pipe-and-filter" class="callout-inner">
-<h3 class="callout-title">Exercise: Pipe and filter<a class="anchor" aria-label="anchor" href="#exercise-pipe-and-filter"></a>
-</h3>
+<h3 class="callout-title">Exercise: Pipe and filter</h3>
 <div class="callout-content">
 <p>Starting with the <code>variants</code> data frame, use pipes to
 subset the data to include only observations from SRR2584863 sample,
@@ -5809,8 +5711,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="exercise" class="callout-inner">
-<h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#exercise"></a>
-</h3>
+<h3 class="callout-title">Exercise</h3>
 <div class="callout-content">
 <p>There are a lot of columns in our data set, so let’s just look at the
 <code>sample_id</code>, <code>POS</code>, <code>QUAL</code>, and
@@ -5910,8 +5811,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <ul>
 <li>How many mutations are INDELs?</li>
@@ -5997,8 +5897,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="grouped-data-frames-in-tidyverse" class="callout-inner">
-<h3 class="callout-title">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a>
-</h3>
+<h3 class="callout-title">Grouped Data Frames in Tidyverse</h3>
 <div class="callout-content">
 <p>When you group a data frame with <code>group_by()</code>, you get a
 grouped data frame. This is a special type of data frame that has all
@@ -6094,8 +5993,7 @@ <h3 id="resources">Resources<a class="anchor" aria-label="anchor" href="#resourc
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>Use the <code>dplyr</code> package to manipulate data frames.</li>
@@ -6166,7 +6064,7 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong><a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
+<section><h2 class="section-heading" id="introduction-to-ggplot2">Introduction to <strong><code>ggplot2</code></strong>
 <a class="anchor" aria-label="anchor" href="#introduction-to-ggplot2"></a>
 </h2>
 <hr class="half-width">
@@ -6206,7 +6104,7 @@ <h3 class="card-title">Objectives</h3>
 or discrete</a>, a quick way to check is to use the <a href="https://www.geeksforgeeks.org/get-summary-of-results-produced-by-functions-in-r-programming-summary-function/" class="external-link"><code>summary()</code></a>
 function. Continuous variables have descriptive statistics but not the
 discrete variables.</p>
-</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code><a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
+</section><section><h2 class="section-heading" id="installing-tidyverse">Installing <code>tidyverse</code>
 <a class="anchor" aria-label="anchor" href="#installing-tidyverse"></a>
 </h2>
 <hr class="half-width">
@@ -6257,7 +6155,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 has been already loaded along with other packages as part of the
 <strong><code>tidyverse</code></strong> framework.</p>
 </section><section><h2 class="section-heading" id="loading-the-dataset">Loading the dataset<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
-<a class="anchor" aria-label="anchor" href="#loading-the-dataset"></a>
 </h2>
 <hr class="half-width">
 <div class="codewrapper sourceCode" id="cb7">
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 <span>  <span class="op">+</span> <span class="fu">geom_point</span><span class="op">(</span><span class="op">)</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="building-your-plots-iteratively">Building your plots iteratively<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
-<a class="anchor" aria-label="anchor" href="#building-your-plots-iteratively"></a>
 </h2>
 <hr class="half-width">
 <p>Building plots with <strong><code>ggplot2</code></strong> is
@@ -6774,8 +6670,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <i class="callout-icon" data-feather="zap"></i>
 </div>
 <div id="challenge" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of mapping quality
 (<code>MQ</code>) over position (<code>POS</code>) with the samples
@@ -6789,7 +6684,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
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 <span>  <span class="fu">theme</span><span class="op">(</span>text <span class="op">=</span> <span class="fu">element_text</span><span class="op">(</span>family <span class="op">=</span> <span class="st">"Bookman"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
 </div>
 <figure><img src="../fig/06-data-visualization-rendered-change-font-family-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure></section><section><h2 class="section-heading" id="faceting">Faceting<a class="anchor" aria-label="anchor" href="#faceting"></a>
-<a class="anchor" aria-label="anchor" href="#faceting"></a>
 </h2>
 <hr class="half-width">
 <p><strong><code>ggplot2</code></strong> has a special technique called
@@ -6874,8 +6768,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="challenge-1" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-1"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use what you just learned to create a scatter plot of PHRED scaled
 quality (<code>QUAL</code>) over position (<code>POS</code>) with the
@@ -6889,7 +6782,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="codewrapper sourceCode" id="cb30">
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 </div>
 </div>
 </section><section><h2 class="section-heading" id="barplots">Barplots<a class="anchor" aria-label="anchor" href="#barplots"></a>
-<a class="anchor" aria-label="anchor" href="#barplots"></a>
 </h2>
 <hr class="half-width">
 <p>We can create barplots using the <a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link"><code>geom_bar</code></a>
@@ -6926,8 +6818,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="challenge-2" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-2"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Since we already have the sample_id labels on the individual plot
 facets, we don’t need the legend. Use the help file for
@@ -6941,7 +6832,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="accordion-body">
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 </div>
 </div>
 </section><section><h2 class="section-heading" id="density">Density<a class="anchor" aria-label="anchor" href="#density"></a>
-<a class="anchor" aria-label="anchor" href="#density"></a>
 </h2>
 <hr class="half-width">
 <p>We can create density plots using the <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
@@ -6977,8 +6867,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="challenge-3" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-3"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>Use <a href="https://ggplot2.tidyverse.org/reference/geom_density.html" class="external-link"><code>geom_density</code></a>
 to plot the distribution of <code>DP</code> with a different fill for
@@ -6991,7 +6880,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7008,7 +6897,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </div>
 </section><section><h2 class="section-heading" id="ggplot2-themes">
 <strong><code>ggplot2</code></strong> themes<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
-<a class="anchor" aria-label="anchor" href="#ggplot2-themes"></a>
 </h2>
 <hr class="half-width">
 <p>In addition to <a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link"><code>theme_bw()</code></a>,
@@ -7032,8 +6920,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 </div>
 <div id="challenge-4" class="callout-inner">
-<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge-4"></a>
-</h3>
+<h3 class="callout-title">Challenge</h3>
 <div class="callout-content">
 <p>With all of this information in hand, please take another five
 minutes to either improve one of the plots generated in this exercise or
@@ -7050,7 +6937,6 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </div>
 </div>
 </section><section><h2 class="section-heading" id="more-ggplot2-plots">More <strong><code>ggplot2</code></strong> Plots<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
-<a class="anchor" aria-label="anchor" href="#more-ggplot2-plots"></a>
 </h2>
 <hr class="half-width">
 <p><strong><code>ggplot2</code></strong> offers many more informative
@@ -7068,7 +6954,6 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link"><code>geom_violin()</code></a>,
 for violin plots</li>
 </ul></section><section><h2 class="section-heading" id="resources">Resources<a class="anchor" aria-label="anchor" href="#resources"></a>
-<a class="anchor" aria-label="anchor" href="#resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
@@ -7089,8 +6974,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>ggplot2 is a powerful tool for high-quality plots</li>
@@ -7139,7 +7023,6 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 <section><h2 class="section-heading" id="getting-help-with-r">Getting help with R<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
-<a class="anchor" aria-label="anchor" href="#getting-help-with-r"></a>
 </h2>
 <hr class="half-width">
 <figure><img src="../fig/oreilly_book_covers.png" alt="rstudio default session" style="width: 600px;" class="figure mx-auto d-block"></figure><p>No matter how much experience you have with R, you will find yourself
@@ -7151,7 +7034,6 @@ <h3 class="card-title">Objectives</h3>
 <p>“Never memorize something that you can look up” -- A. Einstein</p>
 </blockquote>
 </section><section><h2 class="section-heading" id="finding-help-on-stackoverflow-and-biostars">Finding help on Stackoverflow and Biostars<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
-<a class="anchor" aria-label="anchor" href="#finding-help-on-stackoverflow-and-biostars"></a>
 </h2>
 <hr class="half-width">
 <p>Two popular websites will be of great help with many R problems. For
@@ -7165,8 +7047,7 @@ <h3 class="card-title">Objectives</h3>
 <i class="callout-icon" data-feather="bell"></i>
 </div>
 <div id="tip-asking-for-help-using-online-forums" class="callout-inner">
-<h3 class="callout-title">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
-</h3>
+<h3 class="callout-title">Tip: Asking for help using online forums:</h3>
 <div class="callout-content">
 <ul>
 <li>When searching for R help, look for <a href="https://stackoverflow.com/questions/tagged/r" class="external-link">answers with the ‘r’
@@ -7185,7 +7066,6 @@ <h3 class="callout-title">Tip: Asking for help using online forums:<a class="anc
 </div>
 </div>
 </section><section><h2 class="section-heading" id="help-people-help-you">Help people help you<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
-<a class="anchor" aria-label="anchor" href="#help-people-help-you"></a>
 </h2>
 <hr class="half-width">
 <p>Often, in order to duplicate the issue you are having, someone may
@@ -7247,7 +7127,6 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <code class="sourceCode R"><span><span class="fu">saveRDS</span><span class="op">(</span><span class="va">iris</span>, file<span class="op">=</span><span class="st">"iris.rds"</span><span class="op">)</span> <span class="co"># By convention, we use the .rds file extension</span></span></code></pre>
 </div>
 </section><section><h2 class="section-heading" id="final-faqs-on-r">Final FAQs on R<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
-<a class="anchor" aria-label="anchor" href="#final-faqs-on-r"></a>
 </h2>
 <hr class="half-width">
 <p>Finally, here are a few pieces of introductory R knowledge that are
@@ -7310,8 +7189,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <i class="callout-icon" data-feather="key"></i>
 </div>
 <div class="callout-inner">
-<h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="#keypoints1"></a>
-</h3>
+<h3 class="callout-title">Key Points</h3>
 <div class="callout-content">
 <ul>
 <li>R provides thousands of functions for analyzing data, and provides
@@ -7347,7 +7225,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
 
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
 			</div>
 		</footer>
 </div> <!-- / div.container -->
@@ -7370,8 +7248,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/aio.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/aio.html",
   "dateCreated": "2018-03-12",
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diff --git a/instructor/index.html b/instructor/index.html
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-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
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 <div id="prerequisites" class="callout-inner">
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-</h3>
+<h3 class="callout-title">Prerequisites</h3>
 <div class="callout-content">
 <ul><li>
 <strong>Experimenter’s Mindset</strong>: We define the
@@ -496,12 +495,10 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
 option B below where you will only need to <a href="https://figshare.com/articles/Data_Carpentry_Genomics_beta_2_0/7726454" class="external-link">download
 the data files</a> to your local working directory where you will create
 the r-project in.</p>
-<section><h2 class="section-heading" id="r-genomics-workshop-setup-directions">R Genomics workshop setup directions<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a>
-<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a></h2>
+<section><h2 class="section-heading" id="r-genomics-workshop-setup-directions">R Genomics workshop setup directions<a class="anchor" aria-label="anchor" href="#r-genomics-workshop-setup-directions"></a></h2>
 <hr class="half-width"><p>For general setup for the genomics lessons, see that page of <a href="https://datacarpentry.org/genomics-workshop/" class="external-link">the genomics
 workshop</a>.</p>
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-<a class="anchor" aria-label="anchor" href="#installing-r"></a></h2>
+</section><section><h2 class="section-heading" id="installing-r">Installing R<a class="anchor" aria-label="anchor" href="#installing-r"></a></h2>
 <hr class="half-width"><p>This workshop is designed to be run on pre-imaged Amazon Web Services
 (AWS) instances. With the exception of a spreadsheet program, all of the
 software and data used in the workshop are hosted on an Amazon. However,
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+</section><section><h2 class="section-heading" id="installing-rstudio">Installing RStudio<a class="anchor" aria-label="anchor" href="#installing-rstudio"></a></h2>
 <hr class="half-width"><p>The RStudio integrated development environment (IDE) is a popular way
 to use R. We will cover what RStudio is in the lesson. All operating
 systems can go to the Posit LLC <a href="https://posit.co/download/rstudio-desktop/" class="external-link">download pages</a> to
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+            <hr class="half-width lesson-resources">
 <a href="../instructor/aio.html">See all in one page</a>
 
 
@@ -429,7 +429,7 @@ <h1>Instructor Notes</h1>
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diff --git a/instructor/key-points.html b/instructor/key-points.html
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+            <hr class="half-width lesson-resources">
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diff --git a/instructor/profiles.html b/instructor/profiles.html
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-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
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-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -342,7 +342,7 @@ <h1>Learner Profiles</h1>
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 	<div id="to-top">
@@ -364,8 +364,8 @@ <h1>Learner Profiles</h1>
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diff --git a/instructor/reference.html b/instructor/reference.html
index 73535f24..e17c9e2d 100644
--- a/instructor/reference.html
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@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
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-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
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                 <h2 class="accordion-header" id="flush-headingTwelve">
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-            <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="../instructor/aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -346,8 +346,7 @@ <h1>Glossary</h1>
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-<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
 <hr class="half-width"><p>FIXME</p>
 </section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
@@ -385,7 +384,7 @@ <h1>Glossary</h1>
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-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -408,7 +407,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/reference.html",
   "dateCreated": "2018-03-12",
   "dateModified": "2024-07-02",
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diff --git a/key-points.html b/key-points.html
index fc6268b7..f7a37f74 100644
--- a/key-points.html
+++ b/key-points.html
@@ -342,10 +342,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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             <hr class="half-width">
-<div class="accordion accordion-flush resources" id="accordionFlush12">
+<div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources">
+            <hr class="half-width lesson-resources">
 <a href="aio.html">See all in one page</a>
 
 
@@ -488,7 +488,7 @@ <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>
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+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 		</footer>
 </div> <!-- / div.container -->
@@ -511,8 +511,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://datacarpentry.github.io/genomics-r-intro/key-points.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/key-points.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
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diff --git a/pkgdown.yml b/pkgdown.yml
index 19acb500..56236e04 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
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+last_built: 2024-08-27T00:22Z
diff --git a/profiles.html b/profiles.html
index 08a90836..d96c35ef 100644
--- a/profiles.html
+++ b/profiles.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
                     RESOURCES
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@@ -302,7 +302,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                 </div>
               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -342,7 +342,7 @@ <h1>Learner Profiles</h1>
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-        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
+        <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.6" class="external-link">sandpaper (0.16.6)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.4" class="external-link">varnish (1.0.4)</a></p>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -364,8 +364,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/profiles.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/profiles.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-08-20",
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 }
 
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diff --git a/reference.html b/reference.html
index d13858e8..842f4dce 100644
--- a/reference.html
+++ b/reference.html
@@ -279,10 +279,10 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
               </div>
             </div>
 
-            <hr class="half-width"><div class="accordion accordion-flush resources" id="accordionFlush12">
+            <hr class="half-width"><div class="accordion accordion-flush lesson-resources" id="accordionFlush12">
               <div class="accordion-item">
                 <h2 class="accordion-header" id="flush-headingTwelve">
-                  <button class="accordion-button collapsed" id="resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
+                  <button class="accordion-button collapsed" id="lesson-resources" type="button" data-bs-toggle="collapse" data-bs-target="#flush-collapseTwelve" aria-expanded="false" aria-controls="flush-collapseTwelve">
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               </div>
             </div>
-            <hr class="half-width resources"><a href="aio.html">See all in one page</a>
+            <hr class="half-width lesson-resources"><a href="aio.html">See all in one page</a>
 
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
@@ -344,8 +344,7 @@ <h1>Glossary</h1>
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-<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
+<section><h2 class="section-heading" id="glossary">Glossary<a class="anchor" aria-label="anchor" href="#glossary"></a></h2>
 <hr class="half-width"><p>FIXME</p>
 </section></div> <!-- / div.lesson-content -->
     </main><!-- / main#main-content.main-content --><nav class="bottom-pagination mx-md-4" aria-label="Previous and Next Chapter"><div class="d-block d-sm-block d-md-none">
@@ -383,7 +382,7 @@ <h1>Glossary</h1>
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 		</footer></div> <!-- / div.container -->
 	<div id="to-top">
@@ -406,7 +405,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/reference.html",
   "dateCreated": "2018-03-12",
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