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160 lines
6.1 KiB
HTML
160 lines
6.1 KiB
HTML
<!DOCTYPE html>
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<html lang="en-US">
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<head>
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<meta charset="UTF-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<!-- Begin Jekyll SEO tag v2.6.1 -->
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<title>demo-data | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.7" />
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<meta property="og:title" content="demo-data" />
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<meta property="og:locale" content="en_US" />
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<meta name="description" content="Demo datasets" />
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<meta property="og:description" content="Demo datasets" />
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<link rel="canonical" href="https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html" />
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<meta property="og:site_name" content="cellxgene" />
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<script type="application/ld+json">
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{"@type":"WebPage","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"headline":"demo-data","description":"Demo datasets","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=4d1a0c6eaf004182077c1e7585470f6009e3283a">
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<!--[if lt IE 9]>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
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<![endif]-->
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</head>
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<body>
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<div class="wrapper">
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<header>
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<img src="/cellxgene/cellxgene-logo.png" alt="cellxgene" />
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<p>An interactive explorer for single-cell transcriptomics data</p>
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<p>
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<a href="/cellxgene/" class="btn">Quick start</a><br>
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<a href="/cellxgene/posts/install" class="btn">Installation</a><br>
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<a href="/cellxgene/posts/gallery" class="btn">Gallery</a><br>
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<a href="/cellxgene/posts/demo-data" class="btn"><b>Demo datasets</b></a><br>
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<a href="/cellxgene/posts/prepare" class="btn">Preparing your data</a><br>
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<a href="/cellxgene/posts/launch" class="btn">Launching cellxgene</a><br>
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<a href="/cellxgene/posts/hosted" class="btn">Hosting cellxgene</a><br>
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<a href="/cellxgene/posts/annotations" class="btn">Annotating data</a><br>
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<a href="/cellxgene/posts/methods" class="btn">Methods</a><br>
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<a href="/cellxgene/posts/troubleshooting" class="btn">Troubleshooting</a><br>
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<a href="/cellxgene/posts/roadmap" class="btn">Roadmap</a><br>
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<a href="/cellxgene/posts/contribute" class="btn">Contributing (ideas or code)</a><br>
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<a href="/cellxgene/posts/contact" class="btn">Contact & finding help</a><br>
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<a href="/cellxgene/posts/cellxgene_cziscience_com" class="btn">cellxgene.cziscience.com</a><br>
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<a href="https://github.com/chanzuckerberg/cellxgene" class="btn" target="_blank">Code</a>
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</p>
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</header>
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<section>
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<h1 id="example-datasets">Example datasets</h1>
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<p><strong>To use these datasets, run:</strong><br />
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<code class="language-plaintext highlighter-rouge">cellxgene launch [filename.h5ad] --open</code></p>
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<h3 id="peripheral-blood-mononuclear-cells">Peripheral blood mononuclear cells</h3>
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<p>Healthy human PBMCs (10X).</p>
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<ul>
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<li>Source: <a href="https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/pbmc3k">10X genomics</a></li>
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<li>Cells: 2,638</li>
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<li>File size: 19MB</li>
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<li><a href="http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz">Raw data</a></li>
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<li><a href="https://github.com/chanzuckerberg/cellxgene-vignettes/blob/master/dataset-processing/pbmc3k-processing.ipynb">Processing</a></li>
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<li>Launch:
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
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</code></pre></div> </div>
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</li>
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</ul>
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<h3 id="tabula-muris">Tabula muris</h3>
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<p>20 organs and tissues from healthy mice (Smart-Seq2).<br />
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Rich metadata and annotations.</p>
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<ul>
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<li>Source: <a href="https://www.biorxiv.org/content/10.1101/237446v2">bioRxiv, CZBiohub</a></li>
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<li>Cells: 45,423</li>
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<li>File size: 174MB</li>
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<li><a href="https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733">Raw data</a></li>
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<li><a href="https://github.com/chanzuckerberg/cellxgene-vignettes/blob/master/dataset-processing/tabula-muris-processing.ipynb">Processing</a></li>
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<li>Launch:
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://cellxgene-example-data.czi.technology/tabula-muris.h5ad
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</code></pre></div> </div>
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</li>
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</ul>
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<h3 id="tabula-muris-senis">Tabula muris senis</h3>
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<p>22 organs and tissues from healthy mice at ages 3mo, 18mo, 21mo, and 24mo (Smart-Seq2).<br />
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Rich metadata and annotations.</p>
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<ul>
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<li>Source: <a href="https://www.biorxiv.org/content/10.1101/661728v1">bioRxiv, CZBiohub</a></li>
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<li>Cells: 81,478</li>
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<li>File size: 3.9GB</li>
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<li>Raw data [geo link coming soon!]</li>
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<li><a href="https://www.biorxiv.org/content/10.1101/661728v1">Processing</a></li>
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<li>Launch:
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://cellxgene-example-data.czi.technology/tabula-muris-senis.h5ad
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</code></pre></div> </div>
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</li>
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</ul>
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</section>
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<footer>
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<p>This project is maintained by <a href="https://github.com/chanzuckerberg">chanzuckerberg</a></p>
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</footer>
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</div>
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<script src="/cellxgene/assets/js/scale.fix.js"></script>
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</body>
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</html>
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