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0d9f24115c
* fix dead link in launch page * first cut at landing page * wording changes * add additional refinements * fixes from PR review
180 lines
9.2 KiB
HTML
180 lines
9.2 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>demo-data | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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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="http://localhost:4000/cellxgene/posts/launch.html" />
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<meta property="og:url" content="http://localhost:4000/cellxgene/posts/launch.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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{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"http://localhost:4000/cellxgene/posts/launch.html","@context":"http://schema.org"}</script>
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<!-- End Jekyll SEO tag -->
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=88411ae4b44d899609d211ed2db5c41e4fba3068">
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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">Demo datasets</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"><b>Launching cellxgene</b></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="launching-cellxgene-with-your-dataset">Launching cellxgene with your dataset</h1>
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<h2 id="quickstart">Quickstart</h2>
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<p>Once you’ve <a href="prepare">prepared your data</a> for cellxgene, you can launch the app using</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch mydataset.h5ad --open
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</code></pre></div></div>
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<p>You should see your web browser open with the following</p>
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<p><img width="600" src="../images/cellxgene-opening-screenshot.png" pad="50px" /></p>
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<p><strong>Note</strong>: automatic opening of the browser with the <code class="language-plaintext highlighter-rouge">--open</code> flag only works on some platforms (eg, OSX). On other platforms you’ll need to directly point to the provided link in your browser.</p>
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<h2 id="launching-from-a-url">Launching from a URL</h2>
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<p>You can also launch from a URL directly like this:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
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</code></pre></div></div>
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<p>Support for S3 and GCS is not enabled by default. If you wish to directly access S3 or GFS, install one or both of the following packages:</p>
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<ul>
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<li><a href="https://s3fs.readthedocs.io/en/latest/">s3fs</a> for S3 support</li>
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<li><a href="https://gcsfs.readthedocs.io/en/latest/">gcsfs</a> for GCS support</li>
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</ul>
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<p>For example:</p>
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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>pip install s3fs
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cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad
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</code></pre></div></div>
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<h2 id="options-for-cellxgene-launch">Options for cellxgene <code class="language-plaintext highlighter-rouge">launch</code></h2>
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<p><strong>For the most up-to-date and comprehensive list of options, run <code class="language-plaintext highlighter-rouge">cellxgene launch --help</code></strong></p>
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<p><code class="language-plaintext highlighter-rouge">--open</code> automatically opens the web browser after launching (caveat: only works on some operating systems).</p>
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<p><code class="language-plaintext highlighter-rouge">--disable-annotations</code>, <code class="language-plaintext highlighter-rouge">--annotations-file</code> & <code class="language-plaintext highlighter-rouge">--annotations-dir</code> all have to do with creating new categorical annotations in the application. We have a <a href="annotations">whole separate page</a> about their usage! :)</p>
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<p><code class="language-plaintext highlighter-rouge">--diffexp-lfc-cutoff</code> as explained <a href="methods">in the methods</a>, genes are only returned in differential expression if the effect size is above the specified threshold for log fold change. Defaults to 0.01.</p>
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<p><code class="language-plaintext highlighter-rouge">--disable-diffexp</code> will disable and hide the <code class="language-plaintext highlighter-rouge">Compute Differential Expression</code> feature.
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For large datasets, or datasets loaded with the <code class="language-plaintext highlighter-rouge">--backed</code> option, computing differential expression may
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be extremely slow or use excessive resources on the host computer (e.g., memory thrashing).
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Disabling the feature will ensure that this computation is not initiated accidentally.</p>
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<p><code class="language-plaintext highlighter-rouge">--backed</code> option instructs <code class="language-plaintext highlighter-rouge">cellxgene launch</code> to read the H5AD file in “backed” mode (for more information, see the
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<a href="https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html#anndata.read_h5ad">anndata.read_h5ad() documentation</a>).</p>
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<p>By default, cellxgene will read the entire H5AD will be into memory at startup, improving application speed and performance.
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Very large datasets may not fit in memory. The “–backed” mode will read the file incrementally, reducing memory
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use, and for large files, improving startup speed. <em>However</em>, this option will also significantly slow
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down access to gene expression histograms, and may render differential expression calculations too slow
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to use (see <code class="language-plaintext highlighter-rouge">--disable-diffexp</code> for an option to disable this feature).</p>
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<p><code class="language-plaintext highlighter-rouge">--embedding</code> restricts which embeddings will be available in the viewer. By default, all embeddings specified in <code class="language-plaintext highlighter-rouge">anndata.obsm['X_name']</code> will be loaded; if you have many embeddings, you may wish to restrict this list for a speedier launch.</p>
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<p><code class="language-plaintext highlighter-rouge">--title</code> adds a title to the viewer. Defaults to file name.</p>
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<p><code class="language-plaintext highlighter-rouge">--about</code> adds a link where users can go to find more infomation about the dataset. Requires <code class="language-plaintext highlighter-rouge">https</code>.</p>
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<p><code class="language-plaintext highlighter-rouge">--obs-names</code> allows you to specify which column in <code class="language-plaintext highlighter-rouge">anndata.obs</code> to use as <code class="language-plaintext highlighter-rouge">anndata.obs.index</code>.</p>
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<p><code class="language-plaintext highlighter-rouge">--var-names</code> allows you to specify which column in <code class="language-plaintext highlighter-rouge">anndata.var</code> to use as <code class="language-plaintext highlighter-rouge">anndata.var.index</code>.</p>
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<p><code class="language-plaintext highlighter-rouge">--max-category-items</code> omits categorical metadata fields that contain more than N <em>distinct</em> values. Defaults to 1000.</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="/cellxgene/assets/js/scale.fix.js"></script>
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</body>
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</html>
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