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3mmaRand committed Nov 20, 2023
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4 changes: 4 additions & 0 deletions core/core.html
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<a class="nav-link" href="../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-1/overview.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-1/study_after_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-1/study_before_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-1/workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-11/overview.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-11/study_after_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-11/study_before_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-11/workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-2/overview.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-2/study_after_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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80 changes: 42 additions & 38 deletions core/week-2/workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand Down Expand Up @@ -485,58 +489,58 @@ <h1 class="title">Workshop</h1>
<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 212
drwxr-xr-x 2 runner docker 4096 Nov 20 15:17 data
drwxr-xr-x 2 runner docker 4096 Nov 20 15:17 images
-rw-r--r-- 1 runner docker 1597 Nov 20 15:17 overview.qmd
-rw-r--r-- 1 runner docker 25224 Nov 20 15:22 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:17 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70840 Nov 20 15:22 study_before_workshop.html
-rw-r--r-- 1 runner docker 4807 Nov 20 15:17 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13029 Nov 20 15:17 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44938 Nov 20 15:17 workshop.html
-rw-r--r-- 1 runner docker 8550 Nov 20 15:17 workshop.qmd
-rw-r--r-- 1 runner docker 8564 Nov 20 15:22 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4096 Nov 20 15:17 workshop_files</code></pre>
drwxr-xr-x 2 runner docker 4096 Nov 20 15:27 data
drwxr-xr-x 2 runner docker 4096 Nov 20 15:27 images
-rw-r--r-- 1 runner docker 1597 Nov 20 15:27 overview.qmd
-rw-r--r-- 1 runner docker 25383 Nov 20 15:32 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:27 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70840 Nov 20 15:32 study_before_workshop.html
-rw-r--r-- 1 runner docker 4807 Nov 20 15:27 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13029 Nov 20 15:27 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44938 Nov 20 15:27 workshop.html
-rw-r--r-- 1 runner docker 8550 Nov 20 15:27 workshop.qmd
-rw-r--r-- 1 runner docker 8564 Nov 20 15:33 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4096 Nov 20 15:27 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 212K
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:17 data
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:17 images
-rw-r--r-- 1 runner docker 1.6K Nov 20 15:17 overview.qmd
-rw-r--r-- 1 runner docker 25K Nov 20 15:22 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:17 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70K Nov 20 15:22 study_before_workshop.html
-rw-r--r-- 1 runner docker 4.7K Nov 20 15:17 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Nov 20 15:17 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44K Nov 20 15:17 workshop.html
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:17 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:22 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Nov 20 15:17 workshop_files</code></pre>
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:27 data
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:27 images
-rw-r--r-- 1 runner docker 1.6K Nov 20 15:27 overview.qmd
-rw-r--r-- 1 runner docker 25K Nov 20 15:32 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:27 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70K Nov 20 15:32 study_before_workshop.html
-rw-r--r-- 1 runner docker 4.7K Nov 20 15:27 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Nov 20 15:27 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44K Nov 20 15:27 workshop.html
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:27 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:33 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Nov 20 15:27 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 220K
drwxr-xr-x 5 runner docker 4.0K Nov 20 15:22 .
drwxr-xr-x 6 runner docker 4.0K Nov 20 15:21 ..
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:17 data
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:17 images
-rw-r--r-- 1 runner docker 1.6K Nov 20 15:17 overview.qmd
-rw-r--r-- 1 runner docker 25K Nov 20 15:22 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:17 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70K Nov 20 15:22 study_before_workshop.html
-rw-r--r-- 1 runner docker 4.7K Nov 20 15:17 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Nov 20 15:17 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44K Nov 20 15:17 workshop.html
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:17 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:22 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Nov 20 15:17 workshop_files</code></pre>
drwxr-xr-x 5 runner docker 4.0K Nov 20 15:33 .
drwxr-xr-x 6 runner docker 4.0K Nov 20 15:32 ..
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:27 data
drwxr-xr-x 2 runner docker 4.0K Nov 20 15:27 images
-rw-r--r-- 1 runner docker 1.6K Nov 20 15:27 overview.qmd
-rw-r--r-- 1 runner docker 25K Nov 20 15:32 study_after_workshop.html
-rw-r--r-- 1 runner docker 184 Nov 20 15:27 study_after_workshop.qmd
-rw-r--r-- 1 runner docker 70K Nov 20 15:32 study_before_workshop.html
-rw-r--r-- 1 runner docker 4.7K Nov 20 15:27 study_before_workshop.ipynb
-rw-r--r-- 1 runner docker 13K Nov 20 15:27 study_before_workshop.qmd
-rw-r--r-- 1 runner docker 44K Nov 20 15:27 workshop.html
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:27 workshop.qmd
-rw-r--r-- 1 runner docker 8.4K Nov 20 15:33 workshop.rmarkdown
drwxr-xr-x 3 runner docker 4.0K Nov 20 15:27 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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4 changes: 4 additions & 0 deletions core/week-6/overview.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-6/study_after_workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions core/week-6/study_before_workshop.html
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Expand Up @@ -121,6 +121,10 @@
<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand Down
4 changes: 4 additions & 0 deletions core/week-6/workshop.html
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<a class="nav-link" href="../../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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7 changes: 7 additions & 0 deletions images/images.html
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<a class="nav-link" href="../omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link active" href="../images/images.html" rel="" target="" aria-current="page">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand All @@ -163,6 +167,9 @@
<span class="menu-text">Image Data Analysis for Group Project</span></a>
</div>
</li>
<li class="sidebar-item">
<span class="menu-text">Extra help</span>
</li>
</ul>
</div>
</nav><div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
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4 changes: 4 additions & 0 deletions index.html
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<a class="nav-link" href="./omics/omics.html" rel="" target="">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="./images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand Down
4 changes: 4 additions & 0 deletions omics/omics.html
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<a class="nav-link active" href="../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand Down
4 changes: 4 additions & 0 deletions omics/week-3/overview.html
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<a class="nav-link active" href="../../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
Expand Down
4 changes: 4 additions & 0 deletions omics/week-3/study_after_workshop.html
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Expand Up @@ -121,6 +121,10 @@
<a class="nav-link active" href="../../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions omics/week-3/workshop.html
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<a class="nav-link active" href="../../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions omics/week-4/overview.html
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<a class="nav-link active" href="../../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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4 changes: 4 additions & 0 deletions omics/week-4/study_after_workshop.html
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<a class="nav-link active" href="../../omics/omics.html" rel="" target="" aria-current="page">
<span class="menu-text">Omics</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="../../images/images.html" rel="" target="">
<span class="menu-text">Image Analysis</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" rel="" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
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