From 1430c953626dd4125d8d526014567a45ba40a8a1 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 21 May 2024 00:24:16 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : a1bf3ea63447e35256ae721f6e9107bc009f4cc2
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-05-21 00:23:57 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : b22497cb97fa18a9f56b9b5c57dcd41879efc3e2
Branch  : main
Author  : Naupaka Zimmerman <naupaka@gmail.com>
Time    : 2024-05-14 19:58:23 +0000
Message : Merge pull request #275 from datacarpentry/update/packages

Update 13 packages
---
 00-introduction.html                          |  14 ++--
 01-r-basics.html                              |  26 ++++----
 02-data-prelude.html                          |   6 +-
 03-basics-factors-dataframes.html             |  20 +++---
 04-bioconductor-vcfr.html                     |   6 +-
 05-dplyr.html                                 |   6 +-
 06-data-visualization.html                    |   6 +-
 07-r-help.html                                |   6 +-
 404.html                                      |   4 +-
 CODE_OF_CONDUCT.html                          |   6 +-
 LICENSE.html                                  |   6 +-
 aio.html                                      |  62 +++++++++---------
 depth.pdf                                     | Bin 45059 -> 45059 bytes
 discuss.html                                  |   6 +-
 ...-data-visualization-rendered-density-1.png | Bin 9353 -> 9389 bytes
 ...alization-rendered-density-challenge-1.png | Bin 22858 -> 22663 bytes
 images.html                                   |   4 +-
 index.html                                    |  10 +--
 instructor-notes.html                         |   4 +-
 instructor/00-introduction.html               |  14 ++--
 instructor/01-r-basics.html                   |  26 ++++----
 instructor/02-data-prelude.html               |   6 +-
 instructor/03-basics-factors-dataframes.html  |  20 +++---
 instructor/04-bioconductor-vcfr.html          |   6 +-
 instructor/05-dplyr.html                      |   6 +-
 instructor/06-data-visualization.html         |   6 +-
 instructor/07-r-help.html                     |   6 +-
 instructor/404.html                           |   4 +-
 instructor/CODE_OF_CONDUCT.html               |   6 +-
 instructor/LICENSE.html                       |   6 +-
 instructor/aio.html                           |  62 +++++++++---------
 instructor/discuss.html                       |   6 +-
 instructor/images.html                        |   4 +-
 instructor/index.html                         |  10 +--
 instructor/instructor-notes.html              |   4 +-
 instructor/key-points.html                    |   4 +-
 instructor/profiles.html                      |   4 +-
 instructor/reference.html                     |   6 +-
 key-points.html                               |   4 +-
 md5sum.txt                                    |  36 +++++-----
 pkgdown.yml                                   |   2 +-
 profiles.html                                 |   4 +-
 reference.html                                |   6 +-
 43 files changed, 225 insertions(+), 225 deletions(-)

diff --git a/00-introduction.html b/00-introduction.html
index 0f7b66880..30e77e9c4 100644
--- a/00-introduction.html
+++ b/00-introduction.html
@@ -302,7 +302,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -670,7 +670,7 @@ <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
@@ -764,7 +764,7 @@ <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>
@@ -829,7 +829,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> </span>
+<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span>, <span class="va">...</span><span class="op">)</span> </span>
 <span><span class="cn">NULL</span></span></code></pre>
 </div>
 <p><code>round()</code> takes two arguments, <code>x</code>, which is
@@ -911,7 +911,7 @@ <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>
@@ -1014,8 +1014,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/01-r-basics.html b/01-r-basics.html
index 4120e48d1..16159b285 100644
--- a/01-r-basics.html
+++ b/01-r-basics.html
@@ -303,7 +303,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -503,7 +503,7 @@ <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">
@@ -700,7 +700,7 @@ <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 sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -780,7 +780,7 @@ <h3 class="callout-title">Exercise: Create objects and check their class
 <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="cb17">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -948,7 +948,7 @@ <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="#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="cb35">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1199,7 +1199,7 @@ <h3 class="callout-title">Exercise: Examining and subsetting
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#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">
 <ol style="list-style-type: upper-alpha"><li>False - Vectors have both of these properties<br></li>
 <li>True<br></li>
@@ -1428,7 +1428,7 @@ <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="#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="cb76">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1487,7 +1487,7 @@ <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="#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="cb82">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1554,7 +1554,7 @@ <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="#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="cb88">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1599,7 +1599,7 @@ <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="#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="cb90">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1634,7 +1634,7 @@ <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="#collapseSolution10" aria-expanded="false" aria-controls="collapseSolution10">
   <h4 class="accordion-header" id="headingSolution10">Show me the solution</h4>
 </button>
-<div id="collapseSolution10" class="accordion-collapse collapse" data-bs-parent="#accordionSolution10" aria-labelledby="headingSolution10">
+<div id="collapseSolution10" class="accordion-collapse collapse" aria-labelledby="headingSolution10" data-bs-parent="#accordionSolution10">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb92">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1804,8 +1804,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/02-data-prelude.html b/02-data-prelude.html
index 87aae0d3d..2fb0d11ca 100644
--- a/02-data-prelude.html
+++ b/02-data-prelude.html
@@ -295,7 +295,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -606,8 +606,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/03-basics-factors-dataframes.html b/03-basics-factors-dataframes.html
index 96b296114..758d1162d 100644
--- a/03-basics-factors-dataframes.html
+++ b/03-basics-factors-dataframes.html
@@ -302,7 +302,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -441,7 +441,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the<code>read.csv()<
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
@@ -653,7 +653,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -918,11 +918,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </h3>
 <pre class="output" tabindex="0"><code>The following package(s) will be installed:
 - ggplot2 [3.5.1]
-These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu".
+These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.4 milliseconds.</code></pre>
+Successfully installed 1 package in 6.8 milliseconds.</code></pre>
 </div>
 </div>
 </div>
@@ -967,7 +967,7 @@ <h3 class="callout-title">Exercise: Subsetting a data frame<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <ol style="list-style-type: lower-alpha"><li>
 </li></ol><div class="codewrapper sourceCode" id="cb30">
@@ -1660,7 +1660,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb84">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1810,7 +1810,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb91">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1961,8 +1961,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
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diff --git a/04-bioconductor-vcfr.html b/04-bioconductor-vcfr.html
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@@ -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>Using packages from Bioconductor</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -580,8 +580,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/05-dplyr.html b/05-dplyr.html
index 0d3eb35bc..7d58bf50e 100644
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@@ -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>Data Wrangling and Analyses with Tidyverse</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -1542,8 +1542,8 @@ <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/05-dplyr.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/06-data-visualization.html b/06-data-visualization.html
index 6ed2f0ccf..d6cd8c624 100644
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@@ -300,7 +300,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -1248,8 +1248,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/07-r-help.html b/07-r-help.html
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@@ -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>Getting help with R</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -552,8 +552,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/404.html b/404.html
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   "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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
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@@ -280,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -359,8 +359,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/LICENSE.html b/LICENSE.html
index c50e8be83..b625270c1 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -280,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -410,8 +410,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/aio.html b/aio.html
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@@ -336,7 +336,7 @@ <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 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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">
@@ -721,7 +721,7 @@ <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
@@ -818,7 +818,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul>
 <li>
@@ -888,7 +888,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> </span>
+<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span>, <span class="va">...</span><span class="op">)</span> </span>
 <span><span class="cn">NULL</span></span></code></pre>
 </div>
 <p><code>round()</code> takes two arguments, <code>x</code>, which is
@@ -972,7 +972,7 @@ <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">
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1024,7 +1024,7 @@ <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 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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">
@@ -1245,7 +1245,7 @@ <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">
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Here as some possible answers to the challenge:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1470,7 +1470,7 @@ <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">
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-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha">
 <li>False - Vectors have both of these properties<br>
@@ -2262,7 +2262,7 @@ <h3 class="callout-title">Review Exercise 1<a class="anchor" aria-label="anchor"
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 </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 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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 <ol style="list-style-type: upper-alpha">
 <li><p>The <code>read.csv()</code> function has the argument ‘header’
@@ -3290,7 +3290,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
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 <pre class="output" tabindex="0"><code>The following package(s) will be installed:
 - ggplot2 [3.5.1]
-These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu".
+These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.4 milliseconds.</code></pre>
+Successfully installed 1 package in 6.8 milliseconds.</code></pre>
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 </div>
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-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
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@@ -4574,7 +4574,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 </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 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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@@ -7255,8 +7255,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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+        <p>Last updated on 2024-05-21 |
         
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diff --git a/images.html b/images.html
index 1562bc629..aa70d5604 100644
--- a/images.html
+++ b/images.html
@@ -487,8 +487,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 3cad65cd4..6c4ecc322 100644
--- a/index.html
+++ b/index.html
@@ -378,7 +378,7 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Windows</h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Follow the CRAN instructions for downloading the <a href="https://cran.r-project.org/bin/windows/base/" class="external-link">Windows
 Binary</a></p>
@@ -392,7 +392,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler2">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Mac OS X</h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <p>Follow the CRAN instructions for downloading the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">MacOS .pkg file</a>;
 ensure that you download the package that corresponds to your Mac CPU
@@ -408,7 +408,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler3">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Linux</h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <p>Follow the CRAN instructions for your <a href="https://cran.r-project.org/bin/linux/" class="external-link">Linux Distribution</a>; The
 instructions for Ubuntu are <a href="https://cran.r-project.org/bin/linux/ubuntu/" class="external-link">found here</a>.</p>
@@ -473,8 +473,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 48527cab0..e8611312e 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -384,8 +384,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/instructor/00-introduction.html b/instructor/00-introduction.html
index 8a3037e1d..037ebddcb 100644
--- a/instructor/00-introduction.html
+++ b/instructor/00-introduction.html
@@ -302,7 +302,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -672,7 +672,7 @@ <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
@@ -766,7 +766,7 @@ <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>
@@ -831,7 +831,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> </span>
+<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span>, <span class="va">...</span><span class="op">)</span> </span>
 <span><span class="cn">NULL</span></span></code></pre>
 </div>
 <p><code>round()</code> takes two arguments, <code>x</code>, which is
@@ -913,7 +913,7 @@ <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>
@@ -1016,8 +1016,8 @@ <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": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
   </script><script>
diff --git a/instructor/01-r-basics.html b/instructor/01-r-basics.html
index d40204c51..517cd91f0 100644
--- a/instructor/01-r-basics.html
+++ b/instructor/01-r-basics.html
@@ -303,7 +303,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -505,7 +505,7 @@ <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">
@@ -702,7 +702,7 @@ <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 sourceCode" id="cb7">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -782,7 +782,7 @@ <h3 class="callout-title">Exercise: Create objects and check their class
 <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="cb17">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -950,7 +950,7 @@ <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="#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">
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@@ -1806,8 +1806,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/instructor/02-data-prelude.html b/instructor/02-data-prelude.html
index 973b98124..1a75a68e8 100644
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@@ -295,7 +295,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -608,8 +608,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 }
 
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diff --git a/instructor/03-basics-factors-dataframes.html b/instructor/03-basics-factors-dataframes.html
index 6dd763991..9f4a61c41 100644
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@@ -302,7 +302,7 @@ <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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -443,7 +443,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the<code>read.csv()<
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 <div class="accordion-body">
 <ol style="list-style-type: upper-alpha"><li><p>The <code>read.csv()</code> function has the argument ‘header’
 set to TRUE by default, this means the function always assumes the first
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 </h3>
 <pre class="output" tabindex="0"><code>The following package(s) will be installed:
 - ggplot2 [3.5.1]
-These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu".
+These packages will be installed into "~/work/genomics-r-intro/genomics-r-intro/renv/profiles/lesson-requirements/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".
 
 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
-Successfully installed 1 package in 5.4 milliseconds.</code></pre>
+Successfully installed 1 package in 6.8 milliseconds.</code></pre>
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@@ -1812,7 +1812,7 @@ <h3 class="callout-title">Exercise: Putting it all together - data
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@@ -1963,8 +1963,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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index ecfb9b35e..79186d017 100644
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       </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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -582,8 +582,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
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@@ -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>Data Wrangling and Analyses with Tidyverse</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -1544,8 +1544,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Visualization with ggplot2</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -1250,8 +1250,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Getting help with R</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -554,8 +554,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
 }
 
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diff --git a/instructor/404.html b/instructor/404.html
index 84494f211..7338da467 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -344,8 +344,8 @@ <h1>Page not found</h1>
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   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/404.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
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index 065adc170..663472520 100644
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       </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 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -361,8 +361,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
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@@ -280,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -412,8 +412,8 @@ <h1>Licenses</h1>
   "url": "https://datacarpentry.github.io/genomics-r-intro/instructor/LICENSE.html",
   "identifier": "https://datacarpentry.github.io/genomics-r-intro/instructor/LICENSE.html",
   "dateCreated": "2018-03-12",
-  "dateModified": "2024-05-14",
-  "datePublished": "2024-05-14"
+  "dateModified": "2024-05-21",
+  "datePublished": "2024-05-21"
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diff --git a/instructor/aio.html b/instructor/aio.html
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@@ -338,7 +338,7 @@ <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 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -724,7 +724,7 @@ <h3 class="callout-title">Exercise: Work interactively in R<a class="anchor" ari
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <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
@@ -821,7 +821,7 @@ <h3 class="callout-title">Exercise: What do these functions do?<a class="anchor"
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-<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> </span>
+<pre class="output" tabindex="0"><code><span><span class="kw">function</span> <span class="op">(</span><span class="va">x</span>, <span class="va">digits</span> <span class="op">=</span> <span class="fl">0</span>, <span class="va">...</span><span class="op">)</span> </span>
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 <p><code>round()</code> takes two arguments, <code>x</code>, which is
@@ -975,7 +975,7 @@ <h3 class="callout-title">Exercise: Searching for R functions<a class="anchor" a
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 <div class="accordion-body">
 <p>While your search results may return several tests, we list a few you
 might find:</p>
@@ -1027,7 +1027,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -1249,7 +1249,7 @@ <h3 class="callout-title">Exercise: Create some objects in R<a class="anchor" ar
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -3078,7 +3078,7 @@ <h3 class="callout-title">Exercise: Review the arguments of the<code>read.csv()<
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 <ol style="list-style-type: upper-alpha">
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@@ -3296,7 +3296,7 @@ <h3 class="callout-title">Exercise: Revisiting modes and classess<a class="ancho
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 </h3>
 <pre class="output" tabindex="0"><code>The following package(s) will be installed:
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 # Installing packages --------------------------------------------------------
 - Installing ggplot2 ...                        OK [linked from cache]
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@@ -4580,7 +4580,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -4818,7 +4818,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -6029,7 +6029,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -7000,7 +7000,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-05-14 |
+<p>Last updated on 2024-05-21 |
         
         <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>
@@ -7265,8 +7265,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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         <h1>Discussion</h1>
-        <p>Last updated on 2024-05-14 |
+        <p>Last updated on 2024-05-21 |
         
         <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>
         
@@ -354,8 +354,8 @@ <h1>Discussion</h1>
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