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135 lines
4.6 KiB
HTML
135 lines
4.6 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 v2.5.0 -->
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<title>Index | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Index" />
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<meta property="og:locale" content="en_US" />
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<link rel="canonical" href="http://localhost:4000/" />
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<meta property="og:url" content="http://localhost:4000/" />
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<meta property="og:site_name" content="cellxgene" />
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<script type="application/ld+json">
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene-logo.png"}},"@type":"WebSite","url":"http://localhost:4000/","name":"cellxgene","headline":"Index","@context":"http://schema.org"}</script>
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<link rel="stylesheet" href="/assets/css/style.css?v=be9a415a4a06db270354d81837f6e78c71555064">
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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-logo.png" alt="cellxgene" />
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<p></p>
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<p>
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<a href="/" class="btn"><b>Quick start</b></a><br>
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<a href="/posts/install" class="btn">Installation</a><br>
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<a href="/posts/gallery" class="btn">Gallery</a><br>
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<a href="/posts/demo-data" class="btn">Demo datasets</a><br>
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<a href="/posts/prepare" class="btn">Preparing your data</a><br>
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<a href="/posts/launch" class="btn">Launching cellxgene</a><br>
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<a href="/posts/hosted" class="btn">Hosting cellxgene</a><br>
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<a href="/posts/annotations" class="btn">Annotating data</a><br>
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<a href="/posts/methods" class="btn">Methods</a><br>
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<a href="/posts/troubleshooting" class="btn">Troubleshooting</a><br>
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<a href="/posts/roadmap" class="btn">Roadmap</a><br>
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<a href="/posts/contribute" class="btn">Contributing (ideas or code)</a><br>
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<a href="/posts/contact" class="btn">Contact & finding help</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="quick-start">Quick start</h1>
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<p>Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data.</p>
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<p>To install cellxgene you need Python 3.6+. We recommend <a href="/faq.html#how-do-i-create-a-python-environment-for-cellxgene">installing cellxgene into a conda or virtual environment.</a></p>
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<p>Install the package.</p>
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<div class="language-bash highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install cellxgene
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</code></pre></div></div>
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<p>Download an example <a href="https://anndata.readthedocs.io/en/latest/">anndata</a> file</p>
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<div class="language-bash highlighter-rouge"><div class="highlight"><pre class="highlight"><code>curl <span class="nt">-o</span> tabula-muris.h5ad https://cellxgene-example-data.czi.technology/tabula-muris.h5ad.zip
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unzip tabula-muris.h5ad.zip
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</code></pre></div></div>
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<p>Launch cellxgene</p>
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<div class="language-bash highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch tabula-muris.h5ad <span class="nt">--open</span>
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</code></pre></div></div>
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<p>To explore more datasets already formatted for cellxgene, check out the <a href="demo-data">Demo data</a> or
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see <a href="prepare">Preparing your data</a> to learn more about formatting your own
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data for cellxgene.</p>
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<h1 id="getting-help">Getting help</h1>
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<p>We’d love to hear from you!</p>
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<p>For questions, suggestions, or accolades, <a href="https://join-cellxgene-users.herokuapp.com/">join the <code class="highlighter-rouge">#cellxgene-users</code> channel on the CZI Science Slack</a> and say “hi!”.</p>
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<p>For any errors, <a href="https://github.com/chanzuckerberg/cellxgene/issues">report bugs on Github</a>.</p>
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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="/assets/js/scale.fix.js"></script>
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</body>
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</html>
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