From bf6640e52a07337ca27dd738f2a291d65a298b29 Mon Sep 17 00:00:00 2001 From: GitHub Actions <actions@github.com> Date: Tue, 30 Jan 2024 00:43:03 +0000 Subject: [PATCH] site deploy Auto-generated via {sandpaper} Source : ec5313408a27db731f16b3bbc87322892c79522d Branch : md-outputs Author : GitHub Actions <actions@github.com> Time : 2024-01-30 00:42:46 +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 | 30 +++++++++++++++--------------- episode1.html | 8 ++++---- episode2.html | 8 ++++---- episode3.html | 16 ++++++++-------- episode4.html | 6 +++--- episode5.html | 6 +++--- episode6.html | 6 +++--- 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 | 30 +++++++++++++++--------------- instructor/episode1.html | 8 ++++---- instructor/episode2.html | 8 ++++---- instructor/episode3.html | 16 ++++++++-------- instructor/episode4.html | 6 +++--- instructor/episode5.html | 6 +++--- instructor/episode6.html | 6 +++--- 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, 139 insertions(+), 139 deletions(-) diff --git a/404.html b/404.html index b0905dc..ac81c28 100644 --- a/404.html +++ b/404.html @@ -318,8 +318,8 @@ <h1>Page not found</h1> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/404.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/404.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index e12e58c..7459518 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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/LICENSE.html b/LICENSE.html index 0a7abb6..38cb09f 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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/aio.html b/aio.html index 4e7c23c..2eb34a0 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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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"> @@ -465,7 +465,7 @@ <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>The starting point for a machine learning model is processed RNA-Seq data, in the form of count data. This could be raw count data, or TPM or @@ -575,7 +575,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href=" --> </section></section><section id="aio-episode2"><p>Content from <a href="episode2.html">Data Collection: ArrayExpress</a></p> <hr> -<p>Last updated on 2024-01-23 | +<p>Last updated on 2024-01-30 | <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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1"> <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4> </button> -<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1"> +<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="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=" </div> </section></section><section id="aio-episode3"><p>Content from <a href="episode3.html">Data Collection: GEO</a></p> <hr> -<p>Last updated on 2024-01-23 | +<p>Last updated on 2024-01-30 | <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 <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="cb9"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -1362,7 +1362,7 @@ <h3 class="callout-title">Challenge 2: Download the supplementary <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="cb19"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -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" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3"> +<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="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 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1"> <h4 class="accordion-header" id="headingHint1">Give me a hint</h4> </button> -<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1"> +<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1"> <div class="accordion-body"> <p>Hint: you’ll need to refer back to the GEO website to understand how the data has been processed.</p> @@ -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" 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"> <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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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"> @@ -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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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"> @@ -3606,8 +3606,8 @@ <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/aio.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/aio.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode1.html b/episode1.html index 3f1e817..bfcba8f 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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> @@ -405,7 +405,7 @@ <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>The starting point for a machine learning model is processed RNA-Seq data, in the form of count data. This could be raw count data, or TPM or @@ -548,8 +548,8 @@ <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/episode1.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode1.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode2.html b/episode2.html index b173ee6..78124fd 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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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" 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="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": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode3.html b/episode3.html index fec51d4..359216e 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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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" 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="cb9"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -623,7 +623,7 @@ <h3 class="callout-title">Challenge 2: Download the supplementary <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="cb19"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -678,7 +678,7 @@ <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" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3"> +<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="cb21"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -733,7 +733,7 @@ <h3 class="callout-title">Challenge 4:<a class="anchor" aria-label="anchor" href <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1"> <h4 class="accordion-header" id="headingHint1">Give me a hint</h4> </button> -<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1"> +<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1"> <div class="accordion-body"> <p>Hint: you’ll need to refer back to the GEO website to understand how the data has been processed.</p> @@ -746,7 +746,7 @@ <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" 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"> <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=" "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode3.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode3.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode4.html b/episode4.html index 3047d48..9c42733 100644 --- a/episode4.html +++ b/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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> @@ -1231,8 +1231,8 @@ <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/episode4.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode4.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode5.html b/episode5.html index 0596fec..bfa00e8 100644 --- a/episode5.html +++ b/episode5.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: Technical Noise</h1> - <p>Last updated on 2024-01-23 | + <p>Last updated on 2024-01-30 | <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=" "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode5.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode5.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/episode6.html b/episode6.html index caaa848..4f0e361 100644 --- a/episode6.html +++ b/episode6.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: Distribution and Scale</h1> - <p>Last updated on 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> @@ -753,8 +753,8 @@ <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/episode6.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/episode6.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/images.html b/images.html index eaadd61..138926c 100644 --- a/images.html +++ b/images.html @@ -386,8 +386,8 @@ <h3 id="episode6-figure-5">Figure 5</h3> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/images.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/images.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/index.html b/index.html index bf45190..2e25be0 100644 --- a/index.html +++ b/index.html @@ -416,8 +416,8 @@ <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/index.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/index.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor-notes.html b/instructor-notes.html index 508fd34..eab09c5 100644 --- a/instructor-notes.html +++ b/instructor-notes.html @@ -360,8 +360,8 @@ <h1>Instructor Notes</h1> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor-notes.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor-notes.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/404.html b/instructor/404.html index 9597405..78021b3 100644 --- a/instructor/404.html +++ b/instructor/404.html @@ -318,8 +318,8 @@ <h1>Page not found</h1> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/404.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/404.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html index 7e74253..8b20b1c 100644 --- a/instructor/CODE_OF_CONDUCT.html +++ b/instructor/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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/CODE_OF_CONDUCT.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/CODE_OF_CONDUCT.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html index 860e70a..6374a78 100644 --- a/instructor/LICENSE.html +++ b/instructor/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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/LICENSE.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/LICENSE.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/aio.html b/instructor/aio.html index dd929a8..f34d1d7 100644 --- a/instructor/aio.html +++ b/instructor/aio.html @@ -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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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> @@ -468,7 +468,7 @@ <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>The starting point for a machine learning model is processed RNA-Seq data, in the form of count data. This could be raw count data, or TPM or @@ -578,7 +578,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href=" --> </section></section><section id="aio-episode2"><p>Content from <a href="episode2.html">Data Collection: ArrayExpress</a></p> <hr> -<p>Last updated on 2024-01-23 | +<p>Last updated on 2024-01-30 | <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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1"> <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4> </button> -<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1"> +<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="cb4"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -973,7 +973,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href=" </div> </section></section><section id="aio-episode3"><p>Content from <a href="episode3.html">Data Collection: GEO</a></p> <hr> -<p>Last updated on 2024-01-23 | +<p>Last updated on 2024-01-30 | <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 <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="cb9"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -1367,7 +1367,7 @@ <h3 class="callout-title">Challenge 2: Download the supplementary <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="cb19"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -1422,7 +1422,7 @@ <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" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3"> +<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="cb21"> <h3 class="code-label">R<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i> @@ -1477,7 +1477,7 @@ <h3 class="callout-title">Challenge 4:<a class="anchor" aria-label="anchor" href <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1"> <h4 class="accordion-header" id="headingHint1">Give me a hint</h4> </button> -<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1"> +<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1"> <div class="accordion-body"> <p>Hint: you’ll need to refer back to the GEO website to understand how the data has been processed.</p> @@ -1490,7 +1490,7 @@ <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" 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"> <p>The counts data have been normalised and transformed using a variance stabilising transformation using the <code>DESeq2</code> R library.</p> @@ -1528,7 +1528,7 @@ <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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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> @@ -2553,7 +2553,7 @@ <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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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=" --> </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 2024-01-23 | +<p>Last updated on 2024-01-30 | <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> @@ -3657,8 +3657,8 @@ <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/instructor/aio.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/aio.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/episode1.html b/instructor/episode1.html index ae1c62e..31d303f 100644 --- a/instructor/episode1.html +++ b/instructor/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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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> @@ -407,7 +407,7 @@ <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>The starting point for a machine learning model is processed RNA-Seq data, in the form of count data. This could be raw count data, or TPM or @@ -550,8 +550,8 @@ <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/instructor/episode1.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/episode1.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/episode2.html b/instructor/episode2.html index 798fe36..5d69b26 100644 --- a/instructor/episode2.html +++ b/instructor/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 2024-01-23 | + <p>Last updated on 2024-01-30 | <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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1"> <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4> </button> -<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1"> +<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1"> <div class="accordion-body"> <div class="codewrapper sourceCode" id="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=" "url": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/episode2.html", "identifier": "https://carpentries-incubator.github.io/rna-seq-data-for-ml.git/instructor/episode2.html", "dateCreated": "2023-05-23", - "dateModified": "2024-01-23", - "datePublished": "2024-01-23" + "dateModified": "2024-01-30", + "datePublished": "2024-01-30" } </script><script> diff --git a/instructor/episode3.html b/instructor/episode3.html index ed5d2e6..a52db56 100644 --- a/instructor/episode3.html +++ b/instructor/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 2024-01-23 | + <p>Last updated on 2024-01-30 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