From e48a8ff2c45d62bba571a83f55a84f53b7ab5f18 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 6 Feb 2024 00:42:23 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 1ec0ee19b1e9cab388aea339c1f9e15e2c32a29a
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-02-06 00:42:06 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 15cefc1c6aeccad216aecee405d99ab6d5a2809f
Branch  : main
Author  : parkyed <84448128+parkyed@users.noreply.github.com>
Time    : 2023-12-15 14:36:25 +0000
Message : Funding acknowledgement
---
 404.html                         |  4 +--
 CODE_OF_CONDUCT.html             |  6 ++---
 LICENSE.html                     |  6 ++---
 aio.html                         | 40 +++++++++++++++---------------
 episode1.html                    |  6 ++---
 episode2.html                    |  8 +++---
 episode3.html                    | 16 ++++++------
 episode4.html                    | 16 ++++++------
 episode5.html                    |  6 ++---
 episode6.html                    |  8 +++---
 images.html                      |  4 +--
 index.html                       |  4 +--
 instructor-notes.html            |  4 +--
 instructor/404.html              |  4 +--
 instructor/CODE_OF_CONDUCT.html  |  6 ++---
 instructor/LICENSE.html          |  6 ++---
 instructor/aio.html              | 42 ++++++++++++++++----------------
 instructor/episode1.html         |  6 ++---
 instructor/episode2.html         |  8 +++---
 instructor/episode3.html         | 16 ++++++------
 instructor/episode4.html         | 18 +++++++-------
 instructor/episode5.html         |  6 ++---
 instructor/episode6.html         |  8 +++---
 instructor/images.html           |  4 +--
 instructor/index.html            |  4 +--
 instructor/instructor-notes.html |  4 +--
 instructor/key-points.html       |  4 +--
 instructor/profiles.html         |  4 +--
 instructor/reference.html        |  6 ++---
 key-points.html                  |  4 +--
 md5sum.txt                       | 32 ++++++++++++------------
 pkgdown.yml                      |  2 +-
 profiles.html                    |  4 +--
 reference.html                   |  6 ++---
 34 files changed, 161 insertions(+), 161 deletions(-)

diff --git a/404.html b/404.html
index ac81c28..c5a82ab 100644
--- a/404.html
+++ b/404.html
@@ -318,8 +318,8 @@ <h1>Page not found</h1>
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   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/404.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
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diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 7459518..46b9baa 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -256,7 +256,7 @@ <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 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -339,8 +339,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/CODE_OF_CONDUCT.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
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diff --git a/LICENSE.html b/LICENSE.html
index 38cb09f..cb2af96 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -256,7 +256,7 @@ <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 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -390,8 +390,8 @@ <h1>Licenses</h1>
   "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/LICENSE.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 2eb34a0..d4fb95f 100644
--- a/aio.html
+++ b/aio.html
@@ -306,7 +306,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-episode1"><p>Content from <a href="episode1.html">Introduction: Machine Learning Ready RNA-Seq Data</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode1.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -575,7 +575,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 </section></section><section id="aio-episode2"><p>Content from <a href="episode2.html">Data Collection: ArrayExpress</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode2.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -838,7 +838,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -969,7 +969,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 </section></section><section id="aio-episode3"><p>Content from <a href="episode3.html">Data Collection: GEO</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode3.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1215,7 +1215,7 @@ <h3 class="callout-title">Challenge 1: How many samples are in each
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   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb9">
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@@ -1362,7 +1362,7 @@ <h3 class="callout-title">Challenge 2: Download the supplementary
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   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
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 <div class="codewrapper sourceCode" id="cb19">
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@@ -1417,7 +1417,7 @@ <h3 class="callout-title">Challenge 3: Download dataset GSE157657 from
 <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="cb21">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1472,7 +1472,7 @@ <h3 class="callout-title">Challenge 4:<a class="anchor" aria-label="anchor" href
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-<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Hint: you’ll need to refer back to the GEO website to understand how
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@@ -1485,7 +1485,7 @@ <h4 class="accordion-header" id="headingHint1">Give me a hint</h4>
 <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">
 <p>The counts data have been normalised and transformed using a variance
 stabilising transformation using the <code>DESeq2</code> R library.</p>
@@ -1523,7 +1523,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-episode4"><p>Content from <a href="episode4.html">Data Readiness: Data Format and Integrity</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1780,7 +1780,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>All of the checklist items apply in this case. Let’s go through
 them…</p>
@@ -1903,7 +1903,7 @@ <h3 class="callout-title">Challenge 2:<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">
 <ul>
 <li>There is clearly an issue with the coding of the
@@ -2125,7 +2125,7 @@ <h3 class="callout-title">Challenge 3:<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">
 <ul>
 <li>Remove the first row, which is in this case totals of counts for
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 <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">
 <p>We renamed the samples in the sample information to remove spaces, so
 we need to do the same here.</p>
@@ -2430,7 +2430,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
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 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" 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="cb44">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2504,7 +2504,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-episode5"><p>Content from <a href="episode5.html">Data Readiness: Technical Noise</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode5.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -3062,7 +3062,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
  -->
 </section></section><section id="aio-episode6"><p>Content from <a href="episode6.html">Data Readiness: Distribution and Scale</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode6.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -3418,7 +3418,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <table class="table">
 <colgroup>
@@ -3606,8 +3606,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/aio.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
   </script><script>
diff --git a/episode1.html b/episode1.html
index bfcba8f..9acd1e9 100644
--- a/episode1.html
+++ b/episode1.html
@@ -269,7 +269,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction: Machine Learning Ready RNA-Seq Data</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode1.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -548,8 +548,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode1.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
   </script><script>
diff --git a/episode2.html b/episode2.html
index 78124fd..659e962 100644
--- a/episode2.html
+++ b/episode2.html
@@ -270,7 +270,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Collection: ArrayExpress</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode2.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -484,7 +484,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -668,8 +668,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode2.html",
   "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode2.html",
   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
+  "dateModified": "2024-02-06",
+  "datePublished": "2024-02-06"
 }
 
   </script><script>
diff --git a/episode3.html b/episode3.html
index 359216e..5583a2a 100644
--- a/episode3.html
+++ b/episode3.html
@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Collection: GEO</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode3.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -478,7 +478,7 @@ <h3 class="callout-title">Challenge 1: How many samples are in each
 <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">
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@@ -678,7 +678,7 @@ <h3 class="callout-title">Challenge 3: Download dataset GSE157657 from
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 <div class="accordion-body">
 <p>Hint: you’ll need to refer back to the GEO website to understand how
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 <div class="accordion-body">
 <p>The counts data have been normalised and transformed using a variance
 stabilising transformation using the <code>DESeq2</code> R library.</p>
@@ -838,8 +838,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/episode4.html b/episode4.html
index 9c42733..89c3421 100644
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@@ -270,7 +270,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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         <h1>Data Readiness: Data Format and Integrity</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
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 <p>All of the checklist items apply in this case. Let’s go through
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 <ul><li>There is clearly an issue with the coding of the
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 <div class="accordion-body">
 <ul><li>Remove the first row, which is in this case totals of counts for
 each sample</li>
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 <div class="accordion-body">
 <p>We renamed the samples in the sample information to remove spaces, so
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diff --git a/episode5.html b/episode5.html
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         <h1>Data Readiness: Technical Noise</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode5.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -876,8 +876,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/episode6.html b/episode6.html
index 4f0e361..042f032 100644
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Readiness: Distribution and Scale</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode6.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -592,7 +592,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <table class="table"><colgroup><col width="18%"><col width="7%"><col width="7%"><col width="7%"><col width="59%"></colgroup><thead><tr class="header"><th>Model</th>
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@@ -256,7 +256,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -341,8 +341,8 @@ <h1>Contributor Code of Conduct</h1>
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index 6374a78..5416946 100644
--- a/instructor/LICENSE.html
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@@ -256,7 +256,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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         <h1>Licenses</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -392,8 +392,8 @@ <h1>Licenses</h1>
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@@ -308,7 +308,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-episode1"><p>Content from <a href="episode1.html">Introduction: Machine Learning Ready RNA-Seq Data</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode1.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> 11 minutes</p>
@@ -578,7 +578,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode2.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>
@@ -842,7 +842,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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@@ -973,7 +973,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode3.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> 20 minutes</p>
@@ -1220,7 +1220,7 @@ <h3 class="callout-title">Challenge 1: How many samples are in each
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 <div class="codewrapper sourceCode" id="cb9">
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@@ -1367,7 +1367,7 @@ <h3 class="callout-title">Challenge 2: Download the supplementary
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@@ -1422,7 +1422,7 @@ <h3 class="callout-title">Challenge 3: Download dataset GSE157657 from
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-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
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 <p>The counts data have been normalised and transformed using a variance
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@@ -1528,7 +1528,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode4.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> 50 minutes</p>
@@ -1786,7 +1786,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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 <p>All of the checklist items apply in this case. Let’s go through
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 <div class="accordion-body">
 <ul>
 <li>There is clearly an issue with the coding of the
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 <ul>
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@@ -2232,7 +2232,7 @@ <h3 class="callout-title">Challenge 4:<a class="anchor" aria-label="anchor" href
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 <p>We renamed the samples in the sample information to remove spaces, so
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 <p>Here are a number of issues that need addressing in the TB
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 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode5.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> 12 minutes</p>
@@ -3112,7 +3112,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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 </section></section><section id="aio-episode6"><p>Content from <a href="episode6.html">Data Readiness: Distribution and Scale</a></p>
 <hr>
-<p>Last updated on 2024-01-30 |
+<p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode6.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> 12 minutes</p>
@@ -3469,7 +3469,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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 <colgroup>
@@ -3657,8 +3657,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/instructor/episode1.html b/instructor/episode1.html
index 31d303f..3388d5f 100644
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@@ -269,7 +269,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction: Machine Learning Ready RNA-Seq Data</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode1.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -550,8 +550,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2023-05-23",
-  "dateModified": "2024-01-30",
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 }
 
   </script><script>
diff --git a/instructor/episode2.html b/instructor/episode2.html
index 5d69b26..fd61616 100644
--- a/instructor/episode2.html
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@@ -270,7 +270,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Collection: ArrayExpress</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode2.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -486,7 +486,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
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 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -670,8 +670,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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diff --git a/instructor/episode3.html b/instructor/episode3.html
index a52db56..930baec 100644
--- a/instructor/episode3.html
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@@ -271,7 +271,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Collection: GEO</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode3.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -480,7 +480,7 @@ <h3 class="callout-title">Challenge 1: How many samples are in each
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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="cb9">
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@@ -680,7 +680,7 @@ <h3 class="callout-title">Challenge 3: Download dataset GSE157657 from
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 <div class="codewrapper sourceCode" id="cb21">
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@@ -735,7 +735,7 @@ <h3 class="callout-title">Challenge 4:<a class="anchor" aria-label="anchor" href
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+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <div class="accordion-body">
 <p>Hint: you’ll need to refer back to the GEO website to understand how
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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">
 <p>The counts data have been normalised and transformed using a variance
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diff --git a/instructor/episode4.html b/instructor/episode4.html
index d6c6602..3c668ff 100644
--- a/instructor/episode4.html
+++ b/instructor/episode4.html
@@ -270,7 +270,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Readiness: Data Format and Integrity</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
         <a href="https://github.com/carpentries-incubator/rna-seq-data-for-ml.git/edit/main/episodes/episode4.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -504,7 +504,7 @@ <h3 class="callout-title">Challenge 1:<a class="anchor" aria-label="anchor" href
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   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>All of the checklist items apply in this case. Let’s go through
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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>There is clearly an issue with the coding of the
 <code>condition</code> Crohn’s disease. We’ll fix that first, and then
@@ -811,7 +811,7 @@ <h3 class="callout-title">Challenge 3:<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">
 <ul><li>Remove the first row, which is in this case totals of counts for
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 <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">
 <p>We renamed the samples in the sample information to remove spaces, so
 we need to do the same here.</p>
@@ -1060,7 +1060,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
   <h3 class="accordion-header" id="headingInstructor1">
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 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Here are a number of issues that need addressing in the TB
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@@ -1142,7 +1142,7 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i
 <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">Example code to clean up the sample information</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="cb44">
 <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1270,8 +1270,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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-  "dateModified": "2024-01-30",
-  "datePublished": "2024-01-30"
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diff --git a/instructor/episode5.html b/instructor/episode5.html
index d59cb7f..8766014 100644
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@@ -270,7 +270,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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         <h1>Data Readiness: Technical Noise</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
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-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
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         <h1>Reference</h1>
-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
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index abe8fe5..ffc125f 100644
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index 6e1d574..e5772c9 100644
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-        <p>Last updated on 2024-01-30 |
+        <p>Last updated on 2024-02-06 |
         
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