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Quarto GHA Workflow Runner committed Jun 13, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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78 changes: 31 additions & 47 deletions 1_setup.html
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<a class="nav-link active" href="./index.html" aria-current="page">
<span class="menu-text">Home</span></a>
</li>
<li class="nav-item compact">
<a class="nav-link" href="./precourse_preparations.qmd">
<span class="menu-text"></span></a>
<li class="nav-item">
<a class="nav-link" href="./precourse_preparations.html">
<span class="menu-text">Precourse preparations</span></a>
</li>
<li class="nav-item compact">
<a class="nav-link" href="./course_schedule.qmd">
<span class="menu-text"></span></a>
<li class="nav-item">
<a class="nav-link" href="./course_schedule.html">
<span class="menu-text">Course schedule</span></a>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-course-material" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Expand All @@ -138,8 +138,16 @@
<span class="dropdown-text">Quality control</span></a>
</li>
<li>
<a class="dropdown-item" href="./3_integration_clustering.html">
<a class="dropdown-item" href="./3_normalization_scaling.html">
<span class="dropdown-text">Normalization and scaling</span></a>
</li>
<li>
<a class="dropdown-item" href="./4_integration_clustering.html">
<span class="dropdown-text">Integration and clustering</span></a>
</li>
<li>
<a class="dropdown-item" href="./5_marker_gene_identification.html">
<span class="dropdown-text">Marker gene identification</span></a>
</li>
</ul>
</li>
Expand Down Expand Up @@ -232,21 +240,23 @@ <h1 class="title">Setup</h1>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> filtered_feature_bc_matrix.h5 <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_filtered_feature_bc_matrix.h5</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> spatial.tar.gz <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_spatial.tar.gz</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> web_summary.html <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_web_summary.html</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xf</span> spatial.tar.gz</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> spatial.tar.gz</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co"># Posterior</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ../Posterior</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="va">LINK_PREFIX</span><span class="op">=</span>https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Mouse_Brain_Sagittal_Posterior/V1_Mouse_Brain_Sagittal_Posterior</span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> filtered_feature_bc_matrix.h5 <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_filtered_feature_bc_matrix.h5</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> spatial.tar.gz <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_spatial.tar.gz</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> web_summary.html <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_web_summary.html</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xf</span> spatial.tar.gz</span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> spatial.tar.gz</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xf</span> spatial.tar.gz</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> spatial.tar.gz</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="co"># Posterior</span></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ../Posterior</span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="va">LINK_PREFIX</span><span class="op">=</span>https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Mouse_Brain_Sagittal_Posterior/V1_Mouse_Brain_Sagittal_Posterior</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> filtered_feature_bc_matrix.h5 <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_filtered_feature_bc_matrix.h5</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> spatial.tar.gz <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_spatial.tar.gz</span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="ex">curl</span> <span class="at">-o</span> web_summary.html <span class="st">"</span><span class="va">$LINK_PREFIX</span><span class="st">"</span>_web_summary.html</span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xf</span> spatial.tar.gz</span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> spatial.tar.gz</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Have a look at the data directory you have downloaded. It should contain the following:</p>
<p>Have a look at the data directory you have downloaded. It should contain the required data for two slices, the anterior side of a sagittal brain slice, and a posterior side:</p>
<pre><code>course_data/
├── Anterior
│ ├── filtered_feature_bc_matrix.h5
Expand All @@ -270,32 +280,6 @@ <h1 class="title">Setup</h1>
└── web_summary.html

4 directories, 16 files</code></pre>
<p>In this tutorial we are working with two mouse brain slices, the anterior and posterior. The two brain sections represent the sagittal (longitudinal) plane of the mouse brain:</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><img src="assets/images/mouse_brain_sagittal.png" class="img-fluid figure-img"></p>
<figcaption>Mouse brain sagittal</figcaption></figure>
</div>
<p>You can find an interactive map with all brain regions at the <a href="http://atlas.brain-map.org/atlas?atlas=2&amp;plate=100883804#atlas=2&amp;plate=100884129&amp;resolution=19.04&amp;x=7671.818403764205&amp;y=4000&amp;zoom=-4&amp;structure=549">Allen Brain Atlas</a></p>
<p>Our slices contain the anterior and posterior sides of the sagittal section of the mouse brain:</p>
<div>

</div>
<div class="quarto-layout-panel" data-layout-ncol="2">
<div class="quarto-layout-row">
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><img src="raw_data/Anterior/spatial/tissue_lowres_image.png" class="img-fluid figure-img"></p>
<figcaption>Anterior</figcaption></figure>
</div>
</div>
<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><img src="raw_data/Posterior/spatial/tissue_lowres_image.png" class="img-fluid figure-img"></p>
<figcaption>Posterior</figcaption></figure>
</div>
</div>
</div>
</div>
<p>This data is provided by 10x genomics, and further information, like material and methods can be found here:</p>
<ul>
<li>Antherior: <a href="https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0">https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0</a>
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