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albarema authored May 9, 2024
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13 changes: 11 additions & 2 deletions _site/develop/01_RDM_intro.html
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/05_VC.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">5. Data Analysis with Version Control</span></a>
<span class="menu-text">5. Version Control with Git and GitHub</span></a>
</div>
</li>
<li class="sidebar-item">
Expand Down Expand Up @@ -295,7 +295,7 @@ <h1 class="title">1. Introduction to RDM</h1>
<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">April 25, 2024</p>
<p class="date-modified">May 6, 2024</p>
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</div>

Expand Down Expand Up @@ -841,6 +841,15 @@ <h3 class="anchored" data-anchor-id="sources">Sources</h3>
<ul>
<li><a href="https://rdmkit.elixir-europe.org/index">RDMkit</a>: ELIXIR (2021) Research Data Management Kit. A deliverable from the EU-funded ELIXIR-CONVERGE project (grant agreement 871075).</li>
</ul>
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25 changes: 17 additions & 8 deletions _site/develop/02_DMP.html
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<meta name="dcterms.date" content="2023-11-30">

<title>RDM for NGS</title>
<title>RDM for biodata</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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<img src="../img/logo.png" alt="" class="navbar-logo">
</a>
<a class="navbar-brand" href="../index.html">
<span class="navbar-title">RDM for NGS</span>
<span class="navbar-title">RDM for biodata</span>
</a>
</div>
<div id="quarto-search" class="" title="Search"></div>
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/03_DOD.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">3. Best Practices for Data Storage</span></a>
<span class="menu-text">3. Data organization and storage</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/04_metadata.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">4. Metadata for NGS data</span></a>
<span class="menu-text">4. Documentation for biodata</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/05_VC.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">5. Data Analysis with Version Control</span></a>
<span class="menu-text">5. Version Control with Git and GitHub</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/06_pipelines.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">6. Code and Pipelines for Data Analysis</span></a>
<span class="menu-text">6. Processing and analyzing biodata</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/07_repos.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">7. Repositories for biodata</span></a>
<span class="menu-text">7. Storing and sharing biodata</span></a>
</div>
</li>
</ul>
Expand Down Expand Up @@ -261,7 +261,7 @@ <h1 class="title">2. Data Management Plan</h1>
<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">April 17, 2024</p>
<p class="date-modified">May 6, 2024</p>
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</div>

Expand Down Expand Up @@ -403,6 +403,15 @@ <h3 class="anchored" data-anchor-id="sources">Sources</h3>
<li><a href="https://guides.library.stanford.edu/dmps">Stanford University Library Data Management Services website</a></li>
<li><a href="https://rdm.elixir-belgium.org/about_DMP">RDM Guide, Elixir Belgium</a></li>
</ul>
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</section>
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13 changes: 11 additions & 2 deletions _site/develop/03_DOD.html
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/05_VC.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">5. Data Analysis with Version Control</span></a>
<span class="menu-text">5. Version Control with Git and GitHub</span></a>
</div>
</li>
<li class="sidebar-item">
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<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">April 29, 2024</p>
<p class="date-modified">May 6, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -933,6 +933,15 @@ <h3 class="anchored" data-anchor-id="sources">Sources</h3>
<li>Cessda guidelines: <a href="https://dmeg.cessda.eu/Data-Management-Expert-Guide/2.-Organise-Document/File-naming-and-folder-structure" class="uri">https://dmeg.cessda.eu/Data-Management-Expert-Guide/2.-Organise-Document/File-naming-and-folder-structure</a>.</li>
<li>RDMkit Elixir Europe: <a href="https://rdmkit.elixir-europe.org/data_organisation" class="uri">https://rdmkit.elixir-europe.org/data_organisation</a></li>
</ul>
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13 changes: 11 additions & 2 deletions _site/develop/04_metadata.html
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/05_VC.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">5. Data Analysis with Version Control</span></a>
<span class="menu-text">5. Version Control with Git and GitHub</span></a>
</div>
</li>
<li class="sidebar-item">
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<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">May 3, 2024</p>
<p class="date-modified">May 6, 2024</p>
</div>
</div>

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<li><a href="https://pypi.org/project/owlready2/">Owlready2</a>: Python package, enables the loading of ontologies as Python objects. This versatile tool allows users to manipulate and store ontology classes, instances, and properties as needed.</li>
<li><a href="https://shiny.posit.co/">Shiny Apps</a>: easy interactive web apps for data science</li>
</ul>
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37 changes: 20 additions & 17 deletions _site/develop/05_VC.html
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<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../develop/03_DOD.html">Key practices</a></li><li class="breadcrumb-item"><a href="../develop/05_VC.html">5. Data Analysis with Version Control</a></li></ol></nav>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../develop/03_DOD.html">Key practices</a></li><li class="breadcrumb-item"><a href="../develop/05_VC.html">5. Version Control with Git and GitHub</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
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<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../develop/05_VC.html" class="sidebar-item-text sidebar-link active">
<span class="menu-text">5. Data Analysis with Version Control</span></a>
<span class="menu-text">5. Version Control with Git and GitHub</span></a>
</div>
</li>
<li class="sidebar-item">
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<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#data-analysis-best-practices-version-control-with-git-and-github" id="toc-data-analysis-best-practices-version-control-with-git-and-github" class="nav-link active" data-scroll-target="#data-analysis-best-practices-version-control-with-git-and-github">Data Analysis Best Practices: Version Control with Git and GitHub</a>
<ul class="collapse">
<li><a href="#version-control" id="toc-version-control" class="nav-link" data-scroll-target="#version-control">Version control</a>
<li><a href="#best-practices-in-data-analysis" id="toc-best-practices-in-data-analysis" class="nav-link active" data-scroll-target="#best-practices-in-data-analysis">Best Practices in Data Analysis</a>
<ul class="collapse">
<li><a href="#version-control-using-git" id="toc-version-control-using-git" class="nav-link" data-scroll-target="#version-control-using-git">Version control using Git</a></li>
<li><a href="#github-hosting-for-git" id="toc-github-hosting-for-git" class="nav-link" data-scroll-target="#github-hosting-for-git">GitHub Hosting for Git</a></li>
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<ul class="collapse">
<li><a href="#sources" id="toc-sources" class="nav-link" data-scroll-target="#sources">Sources</a></li>
</ul></li>
</ul></li>
</ul>
</nav>
</div>
<!-- main -->
<main class="content" id="quarto-document-content">

<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../develop/03_DOD.html">Key practices</a></li><li class="breadcrumb-item"><a href="../develop/05_VC.html">5. Data Analysis with Version Control</a></li></ol></nav>
<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../develop/03_DOD.html">Key practices</a></li><li class="breadcrumb-item"><a href="../develop/05_VC.html">5. Version Control with Git and GitHub</a></li></ol></nav>
<div class="quarto-title">
<h1 class="title">5. Data Analysis with Version Control</h1>
<h1 class="title">5. Version Control with Git and GitHub</h1>
</div>


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<div>
<div class="quarto-title-meta-heading">Modified</div>
<div class="quarto-title-meta-contents">
<p class="date-modified">May 2, 2024</p>
<p class="date-modified">May 6, 2024</p>
</div>
</div>

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</header>


<section id="data-analysis-best-practices-version-control-with-git-and-github" class="level1">
<h1>Data Analysis Best Practices: Version Control with Git and GitHub</h1>
<div class="callout callout-style-default callout-note callout-titled" title="Course Overview">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
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</ol>
</div>
</div>
<section id="best-practices-in-data-analysis" class="level2">
<h2 class="anchored" data-anchor-id="best-practices-in-data-analysis">Best Practices in Data Analysis</h2>
<p>This lesson introduces version control with Git and Github and its significance in research. You will gain the ability to create Git repositories, and skills to build GitHub pages for showcasing data analysis.</p>
<section id="version-control" class="level2">
<h2 class="anchored" data-anchor-id="version-control">Version control</h2>
<p>Version control systematically tracks project changes, documenting alterations for understanding project evolution. It holds significant importance in research data management, software development, and data analysis, offering numerous advantages.</p>
<div class="callout callout-style-default callout-note callout-titled" title="Advantages of using version control">
<div class="callout-header d-flex align-content-center">
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</section>
<section id="step-by-step-setup-guide" class="level3">
<h3 class="anchored" data-anchor-id="step-by-step-setup-guide">Step-by-Step Setup Guide</h3>
<p>We provide an example of setting up Git, MkDocs, and a GitHub account, enabling you to replicate the process independently! (see <em>Exercise 5</em> in the <a href="../develop/practical_workshop.html">practical material</a>)</p>
<p>We provide an example of setting up Git, Quarto, and a GitHub account, enabling you to replicate the process independently! (see <em>Exercise 5</em> in the <a href="../develop/practical_workshop.html">practical material</a>)</p>
</section>
</section>
<section id="wrap-up" class="level2">
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<section id="sources" class="level3">
<h3 class="anchored" data-anchor-id="sources">Sources</h3>
<ul>
<li><a href="https://guides.library.jhu.edu/c.php?g=1096705&amp;p=8066729">Version Control and Code Repository Link</a>.</li>
<li><a href="https://education.github.com/git-cheat-sheet-education.pdf">Git cheat sheet</a>.</li>
<li><a href="https://guides.library.jhu.edu/c.php?g=1096705&amp;p=8066729">Version Control and Code Repository Link</a></li>
<li><a href="https://education.github.com/git-cheat-sheet-education.pdf">Git cheat sheet</a></li>
</ul>
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</section>
</section>
</section>

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