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3mmaRand committed Oct 2, 2024
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2 changes: 1 addition & 1 deletion core/core.html
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Expand Up @@ -253,7 +253,7 @@ <h1 class="title">Core: Supporting Information</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-1-old/overview.html
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Expand Up @@ -158,7 +158,7 @@ <h1 class="title">Overview</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-1-old/study_after_workshop.html
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Expand Up @@ -158,7 +158,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-1-old/study_before_workshop.html
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Expand Up @@ -151,7 +151,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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4 changes: 2 additions & 2 deletions core/week-1-old/workshop.html
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Expand Up @@ -212,7 +212,7 @@ <h1 class="title">Workshop</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -455,7 +455,7 @@ <h1>Independent study following the workshop</h1>

<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography" id="quarto-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
<div id="ref-baggerly2009" class="csl-entry" role="listitem">
Baggerly, Keith A, and Kevin R Coombes. 2009. <span>“DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY.”</span> <em>Ann. Appl. Stat.</em> 3 (4): 1309–34. <a href="https://doi.org/10.2307/27801549">https://doi.org/10.2307/27801549</a>.
Baggerly, Keith A, and Kevin R Coombes. 2009. <span>“DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY.”</span> <em>Ann. Appl. Stat.</em> 3 (4): 1309–34. <a href="http://www.jstor.org/stable/27801549">http://www.jstor.org/stable/27801549</a>.
</div>
<div id="ref-markowetz2015" class="csl-entry" role="listitem">
Markowetz, Florian. 2015. <span>“Five Selfish Reasons to Work Reproducibly.”</span> <em>Genome Biol.</em> 16 (December): 274. <a href="https://doi.org/10.1186/s13059-015-0850-7">https://doi.org/10.1186/s13059-015-0850-7</a>.
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2 changes: 1 addition & 1 deletion core/week-2-old/overview.html
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Expand Up @@ -149,7 +149,7 @@ <h1 class="title">Overview</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-2-old/study_after_workshop.html
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Expand Up @@ -149,7 +149,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-2-old/study_before_workshop.html
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Expand Up @@ -431,7 +431,7 @@
</div>
</div>

<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</section><section id="overview" class="slide level2"><h2>Overview</h2>
<ul>
<li>RStudio Projects revisited
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76 changes: 40 additions & 36 deletions core/week-2-old/workshop.html
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Expand Up @@ -233,7 +233,7 @@ <h1 class="title">Workshop</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -306,6 +306,7 @@ <h1 class="title">Workshop</h1>
<div class="cell-output cell-output-stdout">
<pre><code>data
images
overview.html
overview.qmd
study_after_workshop.qmd
study_before_workshop.ipynb
Expand All @@ -320,53 +321,56 @@ <h1 class="title">Workshop</h1>
<div class="cell">
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>total 128
drwxr-xr-x 2 runner docker 4096 Sep 18 13:53 data
drwxr-xr-x 2 runner docker 4096 Sep 18 13:53 images
-rw-r--r-- 1 runner docker 1597 Sep 18 13:53 overview.qmd
-rw-r--r-- 1 runner docker 184 Sep 18 13:53 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4807 Sep 18 13:53 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13029 Sep 18 13:53 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 58063 Sep 18 13:53 workshop.html
-rw-r--r-- 1 runner docker 8550 Sep 18 13:53 workshop.qmd
-rw-r--r-- 1 runner docker 8577 Sep 18 13:55 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4096 Sep 18 13:53 workshop_files</code></pre>
<pre><code>total 156
drwxr-xr-x 2 runner docker 4096 Oct 2 14:01 data
drwxr-xr-x 2 runner docker 4096 Oct 2 14:01 images
-rw-r--r-- 1 runner docker 24690 Oct 2 14:12 overview.html
-rw-r--r-- 1 runner docker 1597 Oct 2 14:01 overview.qmd
-rw-r--r-- 1 runner docker 184 Oct 2 14:01 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4807 Oct 2 14:01 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13029 Oct 2 14:01 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 58063 Oct 2 14:01 workshop.html
-rw-r--r-- 1 runner docker 8550 Oct 2 14:01 workshop.qmd
-rw-r--r-- 1 runner docker 8590 Oct 2 14:12 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4096 Oct 2 14:01 workshop_files</code></pre>
</div>
</div>
<p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>total 128K
drwxr-xr-x 2 runner docker 4.0K Sep 18 13:53 data
drwxr-xr-x 2 runner docker 4.0K Sep 18 13:53 images
-rw-r--r-- 1 runner docker 1.6K Sep 18 13:53 overview.qmd
-rw-r--r-- 1 runner docker 184 Sep 18 13:53 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4.7K Sep 18 13:53 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Sep 18 13:53 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 57K Sep 18 13:53 workshop.html
-rw-r--r-- 1 runner docker 8.4K Sep 18 13:53 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Sep 18 13:55 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Sep 18 13:53 workshop_files</code></pre>
<pre><code>total 156K
drwxr-xr-x 2 runner docker 4.0K Oct 2 14:01 data
drwxr-xr-x 2 runner docker 4.0K Oct 2 14:01 images
-rw-r--r-- 1 runner docker 25K Oct 2 14:12 overview.html
-rw-r--r-- 1 runner docker 1.6K Oct 2 14:01 overview.qmd
-rw-r--r-- 1 runner docker 184 Oct 2 14:01 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4.7K Oct 2 14:01 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Oct 2 14:01 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 57K Oct 2 14:01 workshop.html
-rw-r--r-- 1 runner docker 8.4K Oct 2 14:01 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Oct 2 14:12 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Oct 2 14:01 workshop_files</code></pre>
</div>
</div>
<p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>total 136K
drwxr-xr-x 5 runner docker 4.0K Sep 18 13:55 .
drwxr-xr-x 8 runner docker 4.0K Sep 18 13:53 ..
drwxr-xr-x 2 runner docker 4.0K Sep 18 13:53 data
drwxr-xr-x 2 runner docker 4.0K Sep 18 13:53 images
-rw-r--r-- 1 runner docker 1.6K Sep 18 13:53 overview.qmd
-rw-r--r-- 1 runner docker 184 Sep 18 13:53 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4.7K Sep 18 13:53 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Sep 18 13:53 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 57K Sep 18 13:53 workshop.html
-rw-r--r-- 1 runner docker 8.4K Sep 18 13:53 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Sep 18 13:55 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Sep 18 13:53 workshop_files</code></pre>
<pre><code>total 164K
drwxr-xr-x 5 runner docker 4.0K Oct 2 14:12 .
drwxr-xr-x 8 runner docker 4.0K Oct 2 14:01 ..
drwxr-xr-x 2 runner docker 4.0K Oct 2 14:01 data
drwxr-xr-x 2 runner docker 4.0K Oct 2 14:01 images
-rw-r--r-- 1 runner docker 25K Oct 2 14:12 overview.html
-rw-r--r-- 1 runner docker 1.6K Oct 2 14:01 overview.qmd
-rw-r--r-- 1 runner docker 184 Oct 2 14:01 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 4.7K Oct 2 14:01 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Oct 2 14:01 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 57K Oct 2 14:01 workshop.html
-rw-r--r-- 1 runner docker 8.4K Oct 2 14:01 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Oct 2 14:12 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Oct 2 14:01 workshop_files</code></pre>
</div>
</div>
<p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>
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3 changes: 2 additions & 1 deletion core/week-2/overview.html
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Expand Up @@ -251,7 +251,7 @@ <h1 class="title">Overview</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -284,6 +284,7 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
<li><p><a href="../../core/week-2/study_before_workshop.html">Prepare</a></p>
<ol type="i">
<li>📖 Read Understanding file systems</li>
<li>📖 Read Workflow in RStudio</li>
</ol></li>
<li><p><a href="../../core/week-2/workshop.html">Workshop</a></p></li>
<li><p><a href="../../core/week-2/study_after_workshop.html">Consolidate</a></p></li>
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2 changes: 1 addition & 1 deletion core/week-2/study_after_workshop.html
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Expand Up @@ -244,7 +244,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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2 changes: 1 addition & 1 deletion core/week-2/study_before_workshop.html
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Expand Up @@ -244,7 +244,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">18 September, 2024</p>
<p class="date">2 October, 2024</p>
</div>
</div>

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