diff --git a/00-introduction.html b/00-introduction.html
index c89a6915..e66c7b58 100644
--- a/00-introduction.html
+++ b/00-introduction.html
@@ -296,7 +296,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introducing R and RStudio IDE</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/00-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -346,13 +346,12 @@ <h3 class="card-title">Objectives</h3>
 </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 callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-this-lesson-works-best-on-the-cloud">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>
 <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
@@ -430,14 +429,13 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
 you should enter:</p>
 <pre><code>http://ec2.12.2.45.678.compute-1.amazonaws.com:8787</code></pre>
-<div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-sure-there-are-no-spaces-before-or-after-your-url-">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>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -471,14 +469,13 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or
 see an RStudio project file, <strong>dc_genomics_r.Rproj</strong>. All
 RStudio projects end with the “<strong>.Rproj</strong>” file
 extension.</p></li>
-</ol><div id="tip-make-your-project-more-reproducible-with-renv" class="callout callout">
+</ol><div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-your-project-more-reproducible-with-renv">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>
 <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
@@ -543,13 +540,12 @@ <h3 class="callout-title">Tip: Make your project more reproducible with
 installed packages. “Help” will display help files for R functions and
 packages. “Viewer” will allow you to view local web content (e.g. HTML
 outputs).</li>
-</ul><div id="tip-uploads-and-downloads-in-the-cloud" class="callout callout">
+</ul><div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-uploads-and-downloads-in-the-cloud">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a></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
@@ -563,13 +559,12 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 options for pane layout are in the <kbd>View</kbd> menu. Other options
 such as font sizes, colors/themes, and more are in the <kbd>Tools</kbd>
 menu under <kbd>Global Options</kbd>.</p>
-<div id="you-are-working-with-r" class="callout callout">
+<div id="callout5" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="you-are-working-with-r">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a></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
@@ -636,7 +631,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -678,13 +673,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 Congratulations! Although it seems small, knowing what your working
 directory is and being able to set your working directory is the first
 step to analyzing your data.</p>
-<div id="tip-never-use-setwd" class="callout callout">
+<div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-never-use-setwd">Tip: Never use <code>setwd()</code>
+<a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a></h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
 directory is something you need to do, you need to be very careful about
@@ -730,7 +725,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -875,7 +870,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -978,8 +973,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/00-introduction.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/00-introduction.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/01-r-basics.html b/01-r-basics.html
index cf55016a..6374d23f 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
@@ -297,7 +297,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -375,13 +375,12 @@ <h3 class="card-title">Objectives</h3>
 cover plot creation, but will do so using the popular plotting package
 <code>ggplot2</code>)</li>
 <li>How to use advanced R statistical functions</li>
-</ul><div id="tip-where-to-learn-more" class="callout callout">
+</ul><div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-where-to-learn-more">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a></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
@@ -497,7 +496,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -552,14 +551,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 guide</a>, but there is also a <a href="https://google.github.io/styleguide/Rguide.html" class="external-link">Google R style
 guide</a>, and <a href="https://jef.works/R-style-guide/" class="external-link">Jean Fan’s R
 style guide</a>, among others.</p>
-<div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-pay-attention-to-warnings-in-the-script-console">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>
 <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.
@@ -665,7 +663,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -824,7 +822,7 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1075,7 +1073,7 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li>False - Vectors have both of these properties<br></li>
 <li>True<br></li>
@@ -1131,13 +1129,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <td>a or b</td>
 </tr><tr class="odd"><td>a &amp; b</td>
 <td>a and b</td>
-</tr></tbody></table><div id="the-magic-of-programming" class="callout callout">
+</tr></tbody></table><div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="the-magic-of-programming">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a></h3>
 <div class="callout-content">
 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
@@ -1276,7 +1273,7 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb65">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1335,7 +1332,7 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb71">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1402,7 +1399,7 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb77">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1447,7 +1444,7 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb79">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1482,7 +1479,7 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb81">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1499,13 +1496,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-<div id="lists" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="lists">Lists<a class="anchor" aria-label="anchor" href="#lists"></a></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
@@ -1652,8 +1648,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/01-r-basics.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/02-data-prelude.html b/02-data-prelude.html
index c64dcf48..dc764dc7 100644
--- a/02-data-prelude.html
+++ b/02-data-prelude.html
@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to the example dataset and file type</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/02-data-prelude.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -600,8 +600,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/02-data-prelude.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/02-data-prelude.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index 49410610..10430f86 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -296,7 +296,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics continued - factors and data frames</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/03-basics-factors-dataframes.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -379,13 +379,12 @@ <h3 class="card-title">Objectives</h3>
 start to fail (and yes, it can fail for small data sets too). R will
 help you to examine your data so that you can have greater confidence in
 your analysis, and its reproducibility.</p>
-<div id="tip-keep-your-raw-data-separate" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-keep-your-raw-data-separate">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a></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
@@ -457,14 +456,13 @@ <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 help documentation in R. There are many arguments that exist, but which
 we wont have time to cover. Look here to get familiar with functions you
 use frequently, you may be surprised at what you find they can do.</p>
-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-why-does-read-csv-open-the-documentations-to-read-table">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>
 <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
@@ -749,14 +747,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>As you can imagine, this is already useful when you want to generate
 a tally.</p>
-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-treating-objects-as-categories-without-changing-their-mode">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>
 <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
@@ -818,14 +815,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
-<div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-packages-in-r-what-are-they-and-why-do-we-use-them">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>
 <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
@@ -854,7 +850,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.8 milliseconds.</code></pre>
+Successfully installed 1 package in 5.9 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -1296,14 +1292,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </section><section id="coercing-values-in-data-frames"><h2 class="section-heading">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 callout">
+<hr class="half-width"><div id="callout5" 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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames">Tip: coercion isn’t limited to data
+frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a></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
@@ -1511,14 +1506,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 through implicit coercion.</li>
 <li>Check the structure (<code>str()</code>) of your data frames before
 working with them!</li>
-</ul><div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout callout">
+</ul><div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames-1">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>
 <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> ,
@@ -1891,8 +1885,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/03-basics-factors-dataframes.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/04-bioconductor-vcfr.html b/04-bioconductor-vcfr.html
index 4eee0f00..6cc0e4d1 100644
--- a/04-bioconductor-vcfr.html
+++ b/04-bioconductor-vcfr.html
@@ -291,7 +291,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Using packages from Bioconductor</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/04-bioconductor-vcfr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -381,14 +381,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager"><h2 class="section-heading">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>
 </h2>
-<hr class="half-width"><div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout callout">
+<hr class="half-width"><div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies">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>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
 can take a while.</p>
@@ -405,14 +404,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Depending on your particular system, you may need to also allow it to
 install some dependencies or update installed packages in order to
 successfully complete the process.</p>
-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="note-installing-packages-from-bioconductor-vs-from-cran">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>
 <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
@@ -438,14 +436,13 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs
 dataset and not know exactly where to start with analyzing or
 visualizing it. The Bioconductor package search view can be a great way
 to browse through the packages that are available.</p>
-<figure><img src="fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout callout">
+<figure><img src="fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-searching-for-packages-on-the-bioconductor-website">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>
 <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
@@ -477,14 +474,13 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </div>
 </div>
 </div>
-<div id="tip-refreshing-the-rstudio-package-view-after-installing" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-refreshing-the-rstudio-package-view-after-installing">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>
 <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
@@ -574,8 +570,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/04-bioconductor-vcfr.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/04-bioconductor-vcfr.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/05-dplyr.html b/05-dplyr.html
index 56694913..5cdc249e 100644
--- a/05-dplyr.html
+++ b/05-dplyr.html
@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Wrangling and Analyses with Tidyverse</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/05-dplyr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -373,13 +373,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>You only need to install a package once per computer, but you need to
 load it every time you open a new R session and want to use that
 package.</p>
-<div id="tip-installing-packages" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-installing-packages">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a></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
@@ -1357,13 +1356,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 2 SRR2584866    10.6      10        2     79
 3 SRR2589044     9.3       9.5      3     16</code></pre>
 </div>
-<div id="grouped-data-frames-in-tidyverse" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="grouped-data-frames-in-tidyverse">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a></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
@@ -1536,8 +1534,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/05-dplyr.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/05-dplyr.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/06-data-visualization.html b/06-data-visualization.html
index 8428ffcc..d0258061 100644
--- a/06-data-visualization.html
+++ b/06-data-visualization.html
@@ -294,7 +294,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Visualization with ggplot2</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/06-data-visualization.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -705,7 +705,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
+<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
 </div>
 <ul><li>use the <code>ggplot()</code> function and bind the plot to a
 specific data frame using the <code>data</code> argument</li>
@@ -897,7 +897,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -994,7 +994,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1043,7 +1043,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1090,7 +1090,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <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>
@@ -1242,8 +1242,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/06-data-visualization.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/06-data-visualization.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/07-r-help.html b/07-r-help.html
index 8bcc1828..edff282f 100644
--- a/07-r-help.html
+++ b/07-r-help.html
@@ -288,7 +288,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Getting help with R</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/07-r-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -344,13 +344,12 @@ <h3 class="card-title">Objectives</h3>
 “How to do X in R” results from Stack Overflow are usually near the top
 of the list. For <strong>bioinformatics specific questions</strong>, <a href="https://www.biostars.org/" class="external-link">Biostars</a> is a popular online
 forum.</p>
-<div id="tip-asking-for-help-using-online-forums" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-asking-for-help-using-online-forums">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a></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>
@@ -546,8 +545,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/07-r-help.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/07-r-help.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 8c3857cb..9126221e 100644
--- a/404.html
+++ b/404.html
@@ -338,8 +338,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 43ae59d8..c2b53f0d 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -353,8 +353,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/CODE_OF_CONDUCT.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/CODE_OF_CONDUCT.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 07e1e6bb..e1dae648 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -404,8 +404,8 @@ <h1>Licenses</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/LICENSE.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/LICENSE.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index cb960a01..5e1bb29f 100644
--- a/aio.html
+++ b/aio.html
@@ -332,7 +332,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-00-introduction"><p>Content from <a href="00-introduction.html">Introducing R and RStudio IDE</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/00-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -381,12 +381,12 @@ <h3 class="card-title">Objectives</h3>
 <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 callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-this-lesson-works-best-on-the-cloud">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>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
@@ -471,13 +471,13 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
 you should enter:</p>
 <pre><code>http://ec2.12.2.45.678.compute-1.amazonaws.com:8787</code></pre>
-<div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-sure-there-are-no-spaces-before-or-after-your-url-">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>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
@@ -519,12 +519,12 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or
 RStudio projects end with the “<strong>.Rproj</strong>” file
 extension.</p></li>
 </ol>
-<div id="tip-make-your-project-more-reproducible-with-renv" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-your-project-more-reproducible-with-renv">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>
 <div class="callout-content">
@@ -595,12 +595,12 @@ <h3 class="callout-title">Tip: Make your project more reproducible with
 packages. “Viewer” will allow you to view local web content (e.g. HTML
 outputs).</li>
 </ul>
-<div id="tip-uploads-and-downloads-in-the-cloud" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-uploads-and-downloads-in-the-cloud">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a>
 </h3>
 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
@@ -615,12 +615,12 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 options for pane layout are in the <kbd>View</kbd> menu. Other options
 such as font sizes, colors/themes, and more are in the <kbd>Tools</kbd>
 menu under <kbd>Global Options</kbd>.</p>
-<div id="you-are-working-with-r" class="callout callout">
+<div id="callout5" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="you-are-working-with-r">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a>
 </h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
@@ -689,7 +689,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -731,12 +731,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 Congratulations! Although it seems small, knowing what your working
 directory is and being able to set your working directory is the first
 step to analyzing your data.</p>
-<div id="tip-never-use-setwd" class="callout callout">
+<div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-never-use-setwd">Tip: Never use <code>setwd()</code>
+<a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -786,7 +787,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul>
 <li>
@@ -938,7 +939,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -990,7 +991,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-01-r-basics"><p>Content from <a href="01-r-basics.html">R Basics</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1070,12 +1071,12 @@ <h3 class="card-title">Objectives</h3>
 <code>ggplot2</code>)</li>
 <li>How to use advanced R statistical functions</li>
 </ul>
-<div id="tip-where-to-learn-more" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-where-to-learn-more">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
 </h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
@@ -1211,7 +1212,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1271,12 +1272,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 guide</a>, but there is also a <a href="https://google.github.io/styleguide/Rguide.html" class="external-link">Google R style
 guide</a>, and <a href="https://jef.works/R-style-guide/" class="external-link">Jean Fan’s R
 style guide</a>, among others.</p>
-<div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-pay-attention-to-warnings-in-the-script-console">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>
 <div class="callout-content">
@@ -1407,7 +1408,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1591,7 +1592,7 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1845,7 +1846,7 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li>False - Vectors have both of these properties<br>
@@ -1936,12 +1937,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tr>
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+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="the-magic-of-programming">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
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 </div>
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-<div id="lists" class="callout callout">
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 </div>
-<div id="lists" class="callout-inner">
-<h3 class="callout-title">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="lists">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
 </h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
@@ -2409,7 +2410,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-02-data-prelude"><p>Content from <a href="02-data-prelude.html">Introduction to the example dataset and file type</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/02-data-prelude.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2751,7 +2752,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-03-basics-factors-dataframes"><p>Content from <a href="03-basics-factors-dataframes.html">R Basics continued - factors and data frames</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/03-basics-factors-dataframes.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2833,12 +2834,12 @@ <h3 class="card-title">Objectives</h3>
 start to fail (and yes, it can fail for small data sets too). R will
 help you to examine your data so that you can have greater confidence in
 your analysis, and its reproducibility.</p>
-<div id="tip-keep-your-raw-data-separate" class="callout callout">
+<div id="callout1" class="callout">
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 </div>
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-<h3 class="callout-title">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-keep-your-raw-data-separate">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
 </h3>
 <div class="callout-content">
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@@ -2916,13 +2917,13 @@ <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 help documentation in R. There are many arguments that exist, but which
 we wont have time to cover. Look here to get familiar with functions you
 use frequently, you may be surprised at what you find they can do.</p>
-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout callout">
+<div id="callout2" class="callout">
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-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
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-documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-why-does-read-csv-open-the-documentations-to-read-table">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>
 <div class="callout-content">
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 <p>As you can imagine, this is already useful when you want to generate
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-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout callout">
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-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
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+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-treating-objects-as-categories-without-changing-their-mode">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>
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@@ -3283,12 +3284,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <figure><img src="fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
-<div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout callout">
+<div id="callout4" class="callout">
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+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-packages-in-r-what-are-they-and-why-do-we-use-them">Tip: Packages in R – what are they and why do
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 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.8 milliseconds.</code></pre>
+Successfully installed 1 package in 5.9 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -3779,12 +3780,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </section><section id="coercing-values-in-data-frames"><h2 class="section-heading">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 callout">
+<div id="callout5" class="callout">
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 </div>
-<div id="tip-coercion-isnt-limited-to-data-frames" class="callout-inner">
-<h3 class="callout-title">Tip: coercion isn’t limited to data
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames">Tip: coercion isn’t limited to data
 frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
 </h3>
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 <li>Check the structure (<code>str()</code>) of your data frames before
 working with them!</li>
 </ul>
-<div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout callout">
+<div id="callout6" class="callout">
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-<h3 class="callout-title">Tip: coercion isn’t limited to data
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames-1">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>
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 </div>
 </section></section><section id="aio-04-bioconductor-vcfr"><p>Content from <a href="04-bioconductor-vcfr.html">Using packages from Bioconductor</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/04-bioconductor-vcfr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
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 </h2>
 <hr class="half-width">
-<div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout callout">
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-<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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies">Head’s Up: Installing vcfR may take a while
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 <p>Depending on your particular system, you may need to also allow it to
 install some dependencies or update installed packages in order to
 successfully complete the process.</p>
-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout callout">
+<div id="callout2" class="callout">
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 </div>
-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout-inner">
-<h3 class="callout-title">Note: Installing packages from Bioconductor vs
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="note-installing-packages-from-bioconductor-vs-from-cran">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>
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 dataset and not know exactly where to start with analyzing or
 visualizing it. The Bioconductor package search view can be a great way
 to browse through the packages that are available.</p>
-<figure><img src="fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout callout">
+<figure><img src="fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="callout3" class="callout">
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 </div>
-<div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout-inner">
-<h3 class="callout-title">Tip: Searching for packages on the
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-searching-for-packages-on-the-bioconductor-website">Tip: Searching for packages on the
 Bioconductor website<a class="anchor" aria-label="anchor" href="#tip-searching-for-packages-on-the-bioconductor-website"></a>
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 </div>
-<div id="tip-refreshing-the-rstudio-package-view-after-installing" class="callout callout">
+<div id="callout4" class="callout">
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 </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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-refreshing-the-rstudio-package-view-after-installing">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>
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 </div>
 </section></section><section id="aio-05-dplyr"><p>Content from <a href="05-dplyr.html">Data Wrangling and Analyses with Tidyverse</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/05-dplyr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -4653,12 +4654,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>You only need to install a package once per computer, but you need to
 load it every time you open a new R session and want to use that
 package.</p>
-<div id="tip-installing-packages" class="callout callout">
+<div id="callout1" class="callout">
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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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-installing-packages">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
 </h3>
 <div class="callout-content">
 <p>It may be temping to install the <code>tidyverse</code> package, as
@@ -5647,12 +5648,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 2 SRR2584866    10.6      10        2     79
 3 SRR2589044     9.3       9.5      3     16</code></pre>
 </div>
-<div id="grouped-data-frames-in-tidyverse" class="callout callout">
+<div id="callout2" class="callout">
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-<h3 class="callout-title">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="grouped-data-frames-in-tidyverse">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a>
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 <div class="callout-content">
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@@ -5775,7 +5776,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </ol>
 </div></section><section id="aio-06-data-visualization"><p>Content from <a href="06-data-visualization.html">Data Visualization with ggplot2</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/06-data-visualization.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
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 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
+<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
 </div>
 <ul>
 <li>use the <code>ggplot()</code> function and bind the plot to a
@@ -6439,7 +6440,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6538,7 +6539,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb30">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6589,7 +6590,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6638,7 +6639,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <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>
@@ -6745,7 +6746,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-07-r-help"><p>Content from <a href="07-r-help.html">Getting help with R</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/07-r-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -6801,12 +6802,12 @@ <h3 class="card-title">Objectives</h3>
 “How to do X in R” results from Stack Overflow are usually near the top
 of the list. For <strong>bioinformatics specific questions</strong>, <a href="https://www.biostars.org/" class="external-link">Biostars</a> is a popular online
 forum.</p>
-<div id="tip-asking-for-help-using-online-forums" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-asking-for-help-using-online-forums">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
 </h3>
 <div class="callout-content">
 <ul>
@@ -7009,8 +7010,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/depth.pdf b/depth.pdf
index a74939fa..853c00c8 100644
Binary files a/depth.pdf and b/depth.pdf differ
diff --git a/discuss.html b/discuss.html
index 5f0aa338..a8582e9c 100644
--- a/discuss.html
+++ b/discuss.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Discussion</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -346,8 +346,8 @@ <h1>Discussion</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/discuss.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/discuss.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index b51cba33..694318a8 100644
--- a/images.html
+++ b/images.html
@@ -480,8 +480,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 55585853..8e6d51fe 100644
--- a/index.html
+++ b/index.html
@@ -467,8 +467,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index e65e849b..ec7c0c47 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -380,8 +380,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/00-introduction.html b/instructor/00-introduction.html
index d0722d1a..439262a4 100644
--- a/instructor/00-introduction.html
+++ b/instructor/00-introduction.html
@@ -296,7 +296,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introducing R and RStudio IDE</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/00-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -348,13 +348,12 @@ <h3 class="card-title">Objectives</h3>
 </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 callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-this-lesson-works-best-on-the-cloud">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>
 <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
@@ -432,14 +431,13 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
 you should enter:</p>
 <pre><code>http://ec2.12.2.45.678.compute-1.amazonaws.com:8787</code></pre>
-<div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-sure-there-are-no-spaces-before-or-after-your-url-">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>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
 query.</p>
@@ -473,14 +471,13 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or
 see an RStudio project file, <strong>dc_genomics_r.Rproj</strong>. All
 RStudio projects end with the “<strong>.Rproj</strong>” file
 extension.</p></li>
-</ol><div id="tip-make-your-project-more-reproducible-with-renv" class="callout callout">
+</ol><div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-your-project-more-reproducible-with-renv">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>
 <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
@@ -545,13 +542,12 @@ <h3 class="callout-title">Tip: Make your project more reproducible with
 installed packages. “Help” will display help files for R functions and
 packages. “Viewer” will allow you to view local web content (e.g. HTML
 outputs).</li>
-</ul><div id="tip-uploads-and-downloads-in-the-cloud" class="callout callout">
+</ul><div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-uploads-and-downloads-in-the-cloud">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a></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
@@ -565,13 +561,12 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 options for pane layout are in the <kbd>View</kbd> menu. Other options
 such as font sizes, colors/themes, and more are in the <kbd>Tools</kbd>
 menu under <kbd>Global Options</kbd>.</p>
-<div id="you-are-working-with-r" class="callout callout">
+<div id="callout5" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="you-are-working-with-r">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a></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
@@ -638,7 +633,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -680,13 +675,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 Congratulations! Although it seems small, knowing what your working
 directory is and being able to set your working directory is the first
 step to analyzing your data.</p>
-<div id="tip-never-use-setwd" class="callout callout">
+<div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-never-use-setwd">Tip: Never use <code>setwd()</code>
+<a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a></h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
 directory is something you need to do, you need to be very careful about
@@ -732,7 +727,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li>
 <code>dir()</code> # Lists files in the working directory</li>
@@ -877,7 +872,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -980,8 +975,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/00-introduction.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/00-introduction.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/01-r-basics.html b/instructor/01-r-basics.html
index 8cc0e478..8c0772e2 100644
--- a/instructor/01-r-basics.html
+++ b/instructor/01-r-basics.html
@@ -297,7 +297,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -377,13 +377,12 @@ <h3 class="card-title">Objectives</h3>
 cover plot creation, but will do so using the popular plotting package
 <code>ggplot2</code>)</li>
 <li>How to use advanced R statistical functions</li>
-</ul><div id="tip-where-to-learn-more" class="callout callout">
+</ul><div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-where-to-learn-more">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a></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
@@ -499,7 +498,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -554,14 +553,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 guide</a>, but there is also a <a href="https://google.github.io/styleguide/Rguide.html" class="external-link">Google R style
 guide</a>, and <a href="https://jef.works/R-style-guide/" class="external-link">Jean Fan’s R
 style guide</a>, among others.</p>
-<div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-pay-attention-to-warnings-in-the-script-console">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>
 <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.
@@ -667,7 +665,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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@@ -1133,13 +1131,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <td>a or b</td>
 </tr><tr class="odd"><td>a &amp; b</td>
 <td>a and b</td>
-</tr></tbody></table><div id="the-magic-of-programming" class="callout callout">
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+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="the-magic-of-programming">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a></h3>
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 <p>The reason why the expression
 <code>snp_positions[snp_positions &gt; 100000000]</code> works can be
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-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
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 </button>
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@@ -1501,13 +1498,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-<div id="lists" class="callout callout">
+<div id="callout4" class="callout">
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 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="lists">Lists<a class="anchor" aria-label="anchor" href="#lists"></a></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
@@ -1654,8 +1650,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/01-r-basics.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/01-r-basics.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/02-data-prelude.html b/instructor/02-data-prelude.html
index 1741b8a2..4b22bb08 100644
--- a/instructor/02-data-prelude.html
+++ b/instructor/02-data-prelude.html
@@ -289,7 +289,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to the example dataset and file type</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/02-data-prelude.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -602,8 +602,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/03-basics-factors-dataframes.html b/instructor/03-basics-factors-dataframes.html
index 907e0300..bb0ba3e5 100644
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+++ b/instructor/03-basics-factors-dataframes.html
@@ -296,7 +296,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>R Basics continued - factors and data frames</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/03-basics-factors-dataframes.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -381,13 +381,12 @@ <h3 class="card-title">Objectives</h3>
 start to fail (and yes, it can fail for small data sets too). R will
 help you to examine your data so that you can have greater confidence in
 your analysis, and its reproducibility.</p>
-<div id="tip-keep-your-raw-data-separate" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
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-<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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-keep-your-raw-data-separate">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a></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
@@ -459,14 +458,13 @@ <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 help documentation in R. There are many arguments that exist, but which
 we wont have time to cover. Look here to get familiar with functions you
 use frequently, you may be surprised at what you find they can do.</p>
-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout callout">
+<div id="callout2" class="callout">
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-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout-inner">
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-documentations to read.table?<a class="anchor" aria-label="anchor" href="#tip-why-does-read.csv-open-the-documentations-to-read.table"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-why-does-read-csv-open-the-documentations-to-read-table">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>
 <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
@@ -751,14 +749,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>As you can imagine, this is already useful when you want to generate
 a tally.</p>
-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
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-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout-inner">
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-changing their mode<a class="anchor" aria-label="anchor" href="#tip-treating-objects-as-categories-without-changing-their-mode"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-treating-objects-as-categories-without-changing-their-mode">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>
 <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
@@ -820,14 +817,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
-<div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout callout">
+<div id="callout4" class="callout">
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 </div>
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-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-packages-in-r-what-are-they-and-why-do-we-use-them">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>
 <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
@@ -856,7 +852,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.8 milliseconds.</code></pre>
+Successfully installed 1 package in 5.9 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -1298,14 +1294,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </section><section id="coercing-values-in-data-frames"><h2 class="section-heading">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 callout">
+<hr class="half-width"><div id="callout5" class="callout">
 <div class="callout-square">
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 </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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames">Tip: coercion isn’t limited to data
+frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a></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
@@ -1513,14 +1508,13 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 through implicit coercion.</li>
 <li>Check the structure (<code>str()</code>) of your data frames before
 working with them!</li>
-</ul><div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout callout">
+</ul><div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames-1">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>
 <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> ,
@@ -1893,8 +1887,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/03-basics-factors-dataframes.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/03-basics-factors-dataframes.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/04-bioconductor-vcfr.html b/instructor/04-bioconductor-vcfr.html
index 133afcd8..96b69176 100644
--- a/instructor/04-bioconductor-vcfr.html
+++ b/instructor/04-bioconductor-vcfr.html
@@ -291,7 +291,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Using packages from Bioconductor</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/04-bioconductor-vcfr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -383,14 +383,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 </section><section id="second-install-the-vcfr-package-from-bioconductor-using-biocmanager"><h2 class="section-heading">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>
 </h2>
-<hr class="half-width"><div id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies" class="callout callout">
+<hr class="half-width"><div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="heads-up-installing-vcfr-may-take-a-while-due-to-numerous-dependencies">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>
 <div class="callout-content">
 <p>Just be aware that installing packages that have many dependencies
 can take a while.</p>
@@ -407,14 +406,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Depending on your particular system, you may need to also allow it to
 install some dependencies or update installed packages in order to
 successfully complete the process.</p>
-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout callout">
+<div id="callout2" class="callout">
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 </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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="note-installing-packages-from-bioconductor-vs-from-cran">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>
 <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
@@ -440,14 +438,13 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs
 dataset and not know exactly where to start with analyzing or
 visualizing it. The Bioconductor package search view can be a great way
 to browse through the packages that are available.</p>
-<figure><img src="../fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="tip-searching-for-packages-on-the-bioconductor-website" class="callout callout">
+<figure><img src="../fig/bioconductor_search.jpg" alt="screenshot of bioconductor search" class="figure mx-auto d-block"></figure><div id="callout3" class="callout">
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 <i class="callout-icon" data-feather="bell"></i>
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-<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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-searching-for-packages-on-the-bioconductor-website">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>
 <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
@@ -479,14 +476,13 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
 </div>
 </div>
 </div>
-<div id="tip-refreshing-the-rstudio-package-view-after-installing" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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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-installing<a class="anchor" aria-label="anchor" href="#tip-refreshing-the-rstudio-package-view-after-installing"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-refreshing-the-rstudio-package-view-after-installing">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>
 <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
@@ -576,8 +572,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   </script><script>
diff --git a/instructor/05-dplyr.html b/instructor/05-dplyr.html
index dd866797..9ff9d4e3 100644
--- a/instructor/05-dplyr.html
+++ b/instructor/05-dplyr.html
@@ -285,7 +285,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Wrangling and Analyses with Tidyverse</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/05-dplyr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -375,13 +375,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>You only need to install a package once per computer, but you need to
 load it every time you open a new R session and want to use that
 package.</p>
-<div id="tip-installing-packages" class="callout callout">
+<div id="callout1" class="callout">
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-<h3 class="callout-title">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-installing-packages">Tip: Installing packages<a class="anchor" aria-label="anchor" href="#tip-installing-packages"></a></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
@@ -1359,13 +1358,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 2 SRR2584866    10.6      10        2     79
 3 SRR2589044     9.3       9.5      3     16</code></pre>
 </div>
-<div id="grouped-data-frames-in-tidyverse" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
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 </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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="grouped-data-frames-in-tidyverse">Grouped Data Frames in Tidyverse<a class="anchor" aria-label="anchor" href="#grouped-data-frames-in-tidyverse"></a></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
@@ -1538,8 +1536,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/06-data-visualization.html b/instructor/06-data-visualization.html
index 8bd17912..6028fb35 100644
--- a/instructor/06-data-visualization.html
+++ b/instructor/06-data-visualization.html
@@ -294,7 +294,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Visualization with ggplot2</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/06-data-visualization.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -707,7 +707,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
+<pre class="sourceCode r" tabindex="0"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> <span class="sc">&lt;</span>DATA<span class="sc">&gt;</span>, <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="sc">&lt;</span>MAPPINGS<span class="sc">&gt;</span>)) <span class="sc">+</span>  <span class="er">&lt;</span>GEOM_FUNCTION<span class="sc">&gt;</span>()</span></code></pre>
 </div>
 <ul><li>use the <code>ggplot()</code> function and bind the plot to a
 specific data frame using the <code>data</code> argument</li>
@@ -899,7 +899,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="codewrapper sourceCode" id="cb25">
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@@ -996,7 +996,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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@@ -1045,7 +1045,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
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 <div class="codewrapper sourceCode" id="cb32">
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@@ -1092,7 +1092,7 @@ <h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#
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-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb34">
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@@ -1244,8 +1244,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/06-data-visualization.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
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 }
 
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diff --git a/instructor/07-r-help.html b/instructor/07-r-help.html
index 1c0ad1b2..cdcc97fe 100644
--- a/instructor/07-r-help.html
+++ b/instructor/07-r-help.html
@@ -288,7 +288,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Getting help with R</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/07-r-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -346,13 +346,12 @@ <h3 class="card-title">Objectives</h3>
 “How to do X in R” results from Stack Overflow are usually near the top
 of the list. For <strong>bioinformatics specific questions</strong>, <a href="https://www.biostars.org/" class="external-link">Biostars</a> is a popular online
 forum.</p>
-<div id="tip-asking-for-help-using-online-forums" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-asking-for-help-using-online-forums">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a></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>
@@ -548,8 +547,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index ac2b4280..a97b45ab 100644
--- a/instructor/404.html
+++ b/instructor/404.html
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-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 40dfaab7..b7d14353 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -355,8 +355,8 @@ <h1>Contributor Code of Conduct</h1>
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index f901529a..ed40ca9f 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -406,8 +406,8 @@ <h1>Licenses</h1>
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   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/LICENSE.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
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 }
 
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diff --git a/instructor/aio.html b/instructor/aio.html
index acd3263d..d157d6da 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -334,7 +334,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-00-introduction"><p>Content from <a href="00-introduction.html">Introducing R and RStudio IDE</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/00-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -384,12 +384,12 @@ <h3 class="card-title">Objectives</h3>
 <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 callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-this-lesson-works-best-on-the-cloud">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>
 <div class="callout-content">
 <p>Remember, these lessons assume we are using the pre-configured
@@ -474,13 +474,13 @@ <h3 class="callout-title">Discussion: Your experience<a class="anchor" aria-labe
 For example, if your URL was ec2.12.2.45.678.compute-1.amazonaws.com,
 you should enter:</p>
 <pre><code>http://ec2.12.2.45.678.compute-1.amazonaws.com:8787</code></pre>
-<div id="tip-make-sure-there-are-no-spaces-before-or-after-your-url." class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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">
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-after your URL.<a class="anchor" aria-label="anchor" href="#tip-make-sure-there-are-no-spaces-before-or-after-your-url."></a>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-sure-there-are-no-spaces-before-or-after-your-url-">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>
 <div class="callout-content">
 <p>If your URL has spaces, your web browser may interpret it as a search
@@ -522,12 +522,12 @@ <h3 class="callout-title">Tip: Make sure there are no spaces before or
 RStudio projects end with the “<strong>.Rproj</strong>” file
 extension.</p></li>
 </ol>
-<div id="tip-make-your-project-more-reproducible-with-renv" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-make-your-project-more-reproducible-with-renv">Tip: Make your project more reproducible with
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 <div class="callout-content">
@@ -598,12 +598,12 @@ <h3 class="callout-title">Tip: Make your project more reproducible with
 packages. “Viewer” will allow you to view local web content (e.g. HTML
 outputs).</li>
 </ul>
-<div id="tip-uploads-and-downloads-in-the-cloud" class="callout callout">
+<div id="callout4" class="callout">
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-<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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-uploads-and-downloads-in-the-cloud">Tip: Uploads and downloads in the cloud<a class="anchor" aria-label="anchor" href="#tip-uploads-and-downloads-in-the-cloud"></a>
 </h3>
 <div class="callout-content">
 <p>In the “Files” tab you can select a file and download it from your
@@ -618,12 +618,12 @@ <h3 class="callout-title">Tip: Uploads and downloads in the cloud<a class="ancho
 options for pane layout are in the <kbd>View</kbd> menu. Other options
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 menu under <kbd>Global Options</kbd>.</p>
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 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="you-are-working-with-r">You are working with R<a class="anchor" aria-label="anchor" href="#you-are-working-with-r"></a>
 </h3>
 <div class="callout-content">
 <p>Although we won’t be working with R at the terminal, there are lots
@@ -692,7 +692,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>You will get the same output you did as when you ran
 <code>getwd()</code> from the source. You can run any command in the
@@ -734,12 +734,13 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 Congratulations! Although it seems small, knowing what your working
 directory is and being able to set your working directory is the first
 step to analyzing your data.</p>
-<div id="tip-never-use-setwd" class="callout callout">
+<div id="callout6" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-never-use-setwd">Tip: Never use <code>setwd()</code>
+<a class="anchor" aria-label="anchor" href="#tip-never-use-setwd"></a>
 </h3>
 <div class="callout-content">
 <p>Wait, what was the last 2 minutes about? Well, setting your working
@@ -789,7 +790,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul>
 <li>
@@ -941,7 +942,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -993,7 +994,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-01-r-basics"><p>Content from <a href="01-r-basics.html">R Basics</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/01-r-basics.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 80 minutes</p>
@@ -1074,12 +1075,12 @@ <h3 class="card-title">Objectives</h3>
 <code>ggplot2</code>)</li>
 <li>How to use advanced R statistical functions</li>
 </ul>
-<div id="tip-where-to-learn-more" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-where-to-learn-more">Tip: Where to learn more<a class="anchor" aria-label="anchor" href="#tip-where-to-learn-more"></a>
 </h3>
 <div class="callout-content">
 <p>The following are good resources for learning more about R. Some of
@@ -1215,7 +1216,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1275,12 +1276,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 guide</a>, but there is also a <a href="https://google.github.io/styleguide/Rguide.html" class="external-link">Google R style
 guide</a>, and <a href="https://jef.works/R-style-guide/" class="external-link">Jean Fan’s R
 style guide</a>, among others.</p>
-<div id="tip-pay-attention-to-warnings-in-the-script-console" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-pay-attention-to-warnings-in-the-script-console">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>
 <div class="callout-content">
@@ -1411,7 +1412,7 @@ <h3 class="callout-title">Exercise: Create objects and check their
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1595,7 +1596,7 @@ <h3 class="callout-title">Exercise: Compute the golden ratio<a class="anchor" ar
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1849,7 +1850,7 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li>False - Vectors have both of these properties<br>
@@ -1940,12 +1941,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </tr>
 </tbody>
 </table>
-<div id="the-magic-of-programming" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="the-magic-of-programming">The magic of programming<a class="anchor" aria-label="anchor" href="#the-magic-of-programming"></a>
 </h3>
 <div class="callout-content">
 <p>The reason why the expression
@@ -2086,7 +2087,7 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb65">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2145,7 +2146,7 @@ <h3 class="callout-title">Review Exercise 2<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6">Show me the solution</h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb71">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2215,7 +2216,7 @@ <h3 class="callout-title">Review Exercise 3<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7">Show me the solution</h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb77">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2262,7 +2263,7 @@ <h3 class="callout-title">Review Exercise 4<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8">Show me the solution</h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb79">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2297,7 +2298,7 @@ <h3 class="callout-title">Review Exercise 5<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9">Show me the solution</h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb81">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2314,12 +2315,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-<div id="lists" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="lists">Lists<a class="anchor" aria-label="anchor" href="#lists"></a>
 </h3>
 <div class="callout-content">
 <p>Lists are quite useful in R, but we won’t be using them in the
@@ -2413,7 +2414,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-02-data-prelude"><p>Content from <a href="02-data-prelude.html">Introduction to the example dataset and file type</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/02-data-prelude.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 15 minutes</p>
@@ -2756,7 +2757,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-03-basics-factors-dataframes"><p>Content from <a href="03-basics-factors-dataframes.html">R Basics continued - factors and data frames</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/03-basics-factors-dataframes.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 90 minutes</p>
@@ -2839,12 +2840,12 @@ <h3 class="card-title">Objectives</h3>
 start to fail (and yes, it can fail for small data sets too). R will
 help you to examine your data so that you can have greater confidence in
 your analysis, and its reproducibility.</p>
-<div id="tip-keep-your-raw-data-separate" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-keep-your-raw-data-separate">Tip: Keep your raw data separate<a class="anchor" aria-label="anchor" href="#tip-keep-your-raw-data-separate"></a>
 </h3>
 <div class="callout-content">
 <p>When you work with data in R, you are not changing the original file
@@ -2922,13 +2923,13 @@ <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 help documentation in R. There are many arguments that exist, but which
 we wont have time to cover. Look here to get familiar with functions you
 use frequently, you may be surprised at what you find they can do.</p>
-<div id="tip-why-does-read.csv-open-the-documentations-to-read.table" class="callout callout">
+<div id="callout2" class="callout">
 <div class="callout-square">
 <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>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-why-does-read-csv-open-the-documentations-to-read-table">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>
 <div class="callout-content">
 <p>The reason for this is because <code>read.csv</code> is actually a
@@ -3217,12 +3218,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 <p>As you can imagine, this is already useful when you want to generate
 a tally.</p>
-<div id="tip-treating-objects-as-categories-without-changing-their-mode" class="callout callout">
+<div id="callout3" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-treating-objects-as-categories-without-changing-their-mode">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>
 <div class="callout-content">
@@ -3289,12 +3290,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <figure><img src="../fig/03-basics-factors-dataframes-rendered-unnamed-chunk-16-1.png" style="display: block; margin: auto;" class="figure mx-auto d-block"></figure><p>Factors come in handy in many places when using R. Even using more
 sophisticated plotting packages such as ggplot2 will sometimes require
 you to understand how to manipulate factors.</p>
-<div id="tip-packages-in-r-what-are-they-and-why-do-we-use-them" class="callout callout">
+<div id="callout4" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-packages-in-r-what-are-they-and-why-do-we-use-them">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>
 <div class="callout-content">
@@ -3325,7 +3326,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.8 milliseconds.</code></pre>
+Successfully installed 1 package in 5.9 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -3785,12 +3786,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </section><section id="coercing-values-in-data-frames"><h2 class="section-heading">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 callout">
+<div id="callout5" 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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames">Tip: coercion isn’t limited to data
 frames<a class="anchor" aria-label="anchor" href="#tip-coercion-isnt-limited-to-data-frames"></a>
 </h3>
 <div class="callout-content">
@@ -4003,12 +4004,12 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <li>Check the structure (<code>str()</code>) of your data frames before
 working with them!</li>
 </ul>
-<div id="tip-coercion-isnt-limited-to-data-frames-1" class="callout callout">
+<div id="callout6" class="callout">
 <div class="callout-square">
 <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
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="tip-coercion-isnt-limited-to-data-frames-1">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>
 <div class="callout-content">
@@ -4334,7 +4335,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-bioconductor-vcfr"><p>Content from <a href="04-bioconductor-vcfr.html">Using packages from Bioconductor</a></p>
 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/04-bioconductor-vcfr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 13 minutes</p>
@@ -4427,12 +4428,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 <hr class="half-width">
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+<div class="section level3 callout-title callout-inner">
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@@ -4451,12 +4452,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <p>Depending on your particular system, you may need to also allow it to
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-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout callout">
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-<div id="note-installing-packages-from-bioconductor-vs-from-cran" class="callout-inner">
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+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="note-installing-packages-from-bioconductor-vs-from-cran">Note: Installing packages from Bioconductor vs
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@@ -4485,12 +4486,12 @@ <h3 class="callout-title">Note: Installing packages from Bioconductor vs
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 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/05-dplyr.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 55 minutes</p>
@@ -4661,12 +4662,12 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
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 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/06-data-visualization.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 90 minutes</p>
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 <hr>
-<p>Last updated on 2024-02-27 |
+<p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/episodes/07-r-help.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 15 minutes</p>
@@ -6811,12 +6812,12 @@ <h3 class="card-title">Objectives</h3>
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+<h3 class="callout-title" id="tip-asking-for-help-using-online-forums">Tip: Asking for help using online forums:<a class="anchor" aria-label="anchor" href="#tip-asking-for-help-using-online-forums"></a>
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-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/learners/discuss.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
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-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
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diff --git a/pkgdown.yml b/pkgdown.yml
index 7d94b2de..8039a6ee 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,6 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-02-27T00:24Z
+last_built: 2024-03-05T00:10Z
 
diff --git a/profiles.html b/profiles.html
index 8c52a753..1000ef7c 100644
--- a/profiles.html
+++ b/profiles.html
@@ -305,8 +305,8 @@ <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": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
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diff --git a/reference.html b/reference.html
index 1c1220f0..3cad91bc 100644
--- a/reference.html
+++ b/reference.html
@@ -274,7 +274,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Glossary</h1>
-        <p>Last updated on 2024-02-27 |
+        <p>Last updated on 2024-03-05 |
         
         <a href="https://github.com/datacarpentry/genomics-r-intro/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -346,8 +346,8 @@ <h1>Glossary</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/reference.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/reference.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateModified": "2024-03-05",
+  "datePublished": "2024-03-05"
 }
 
   </script><script>