mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Change default branch from 'master' to 'main' (#1589)
The default branch has been changed. This PR cleans up references to `master` and fixes links that would otherwise be broken. For more background see the following references: * https://www.independent.co.uk/life-style/gadgets-and-tech/news/github-master-slave-slavery-whitelist-language-inclusive-a9568576.html * https://tools.ietf.org/id/draft-knodel-terminology-00.html
This commit is contained in:
Matt Weiden
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>Index | cellxgene</title>
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<meta property="og:title" content="Index" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/" />
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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":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebSite","url":"https://chanzuckerberg.github.io/cellxgene/","headline":"Index","name":"cellxgene","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>annotations | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="annotations" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/annotations.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":"Creating annotations","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"annotations","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Creating annotations","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","headline":"annotations","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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>Contact | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Contact" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/contact.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":"Contact","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Contact","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Contact","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","headline":"Contact","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<title>Code of conduct | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Code of conduct" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/contribute.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":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Code of conduct","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","headline":"Code of conduct","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<!-- 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 v3.8.5" />
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<meta property="og:title" content="demo-data" />
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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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{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Demo datasets","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","headline":"demo-data","@context":"https://schema.org"}</script>
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<!-- Begin Jekyll SEO tag v2.6.1 -->
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<title>Gallery | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Gallery" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/gallery.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":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Gallery","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","headline":"Gallery","@context":"https://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=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<!-- Begin Jekyll SEO tag v2.6.1 -->
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<title>Hosting cellxgene on the web | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Hosting cellxgene on the web" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/hosted.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":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Hosting cellxgene on the web","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","headline":"Hosting cellxgene on the web","@context":"https://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=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<!-- Begin Jekyll SEO tag v2.6.1 -->
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<title>Install | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Install" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/install.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":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Install","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","headline":"Install","@context":"https://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=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<!-- 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 v3.8.5" />
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<meta property="og:title" content="demo-data" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/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":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Demo datasets","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","headline":"demo-data","@context":"https://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=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<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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<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/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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<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>Methods | cellxgene</title>
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<meta name="generator" content="Jekyll v3.8.5" />
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<meta property="og:title" content="Methods" />
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<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/methods.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":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Methods","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","@context":"http://schema.org"}</script>
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{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","headline":"Methods","@context":"https://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=994a7b19bb6437b8e48d92683aab7fd8077477f7">
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<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
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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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<h2 id="differential-expression">Differential expression</h2>
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<p>We’re actively working on how to improve differential expression within the app.
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<strong>N.B.: the <a href="https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40">current implementation</a> assumes normally distributed values on a linear scale.</strong></p>
|
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<strong>N.B.: the <a href="https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40">current implementation</a> assumes normally distributed values on a linear scale.</strong></p>
|
||||
|
||||
<p>Currently, we use a <a href="https://en.wikipedia.org/wiki/Welch%27s_t-test">Welch’s <em>t</em>-test</a>, which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have <strong>equal</strong> means. P-values are adjusted with the <a href="https://en.wikipedia.org/wiki/Bonferroni_correction">Bonferroni corrrection</a>.</p>
|
||||
|
||||
|
||||
@@ -17,7 +17,7 @@ cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in `
|
||||
## Differential expression
|
||||
|
||||
We're actively working on how to improve differential expression within the app.
|
||||
**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
|
||||
**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
|
||||
|
||||
Currently, we use a [Welch's _t_-test](https://en.wikipedia.org/wiki/Welch%27s_t-test), which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have **equal** means. P-values are adjusted with the [Bonferroni corrrection](https://en.wikipedia.org/wiki/Bonferroni_correction).
|
||||
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||||
|
||||
<!-- Begin Jekyll SEO tag v2.5.0 -->
|
||||
<!-- Begin Jekyll SEO tag v2.6.1 -->
|
||||
<title>prepare | cellxgene</title>
|
||||
<meta name="generator" content="Jekyll v3.8.5" />
|
||||
<meta property="og:title" content="prepare" />
|
||||
@@ -16,10 +16,10 @@
|
||||
<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/prepare.html" />
|
||||
<meta property="og:site_name" content="cellxgene" />
|
||||
<script type="application/ld+json">
|
||||
{"description":"Preparing your data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"prepare","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","@context":"http://schema.org"}</script>
|
||||
{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Preparing your data","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","headline":"prepare","@context":"https://schema.org"}</script>
|
||||
<!-- End Jekyll SEO tag -->
|
||||
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<![endif]-->
|
||||
@@ -103,7 +103,7 @@
|
||||
<li>Expression values (raw or normalized) in <code class="language-plaintext highlighter-rouge">anndata.X</code></li>
|
||||
<li>At least one embedding (e.g., tSNE, UMAP) in <code class="language-plaintext highlighter-rouge">anndata.obsm</code>, specified with the prefix <code class="language-plaintext highlighter-rouge">X_</code> (e.g., by default scanpy stores UMAP coordinates in <code class="language-plaintext highlighter-rouge">anndata.obsm['X_umap']</code>)</li>
|
||||
<li>A unique identifier is required for each cell, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">obs</code> DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--obs-names</code></li>
|
||||
<li>A unique identifier is required for each gene, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">var</code> DataFrame index. If the index is not unique or does not contain the cell ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--var-names</code></li>
|
||||
<li>A unique identifier is required for each gene, which by default will be pulled from the <code class="language-plaintext highlighter-rouge">var</code> DataFrame index. If the index is not unique or does not contain the gene ID, an alternative column can be specified with <code class="language-plaintext highlighter-rouge">--var-names</code></li>
|
||||
</ul>
|
||||
|
||||
<h4 id="what-about-r-objects-from-seurat--bioconductor">What about R objects from seurat / bioconductor!?</h4>
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||||
|
||||
<!-- Begin Jekyll SEO tag v2.5.0 -->
|
||||
<!-- Begin Jekyll SEO tag v2.6.1 -->
|
||||
<title>roadmap | cellxgene</title>
|
||||
<meta name="generator" content="Jekyll v3.8.5" />
|
||||
<meta property="og:title" content="roadmap" />
|
||||
@@ -16,10 +16,10 @@
|
||||
<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html" />
|
||||
<meta property="og:site_name" content="cellxgene" />
|
||||
<script type="application/ld+json">
|
||||
{"description":"Roadmap","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"roadmap","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","@context":"http://schema.org"}</script>
|
||||
{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Roadmap","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","headline":"roadmap","@context":"https://schema.org"}</script>
|
||||
<!-- End Jekyll SEO tag -->
|
||||
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<![endif]-->
|
||||
|
||||
@@ -5,7 +5,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||||
|
||||
<!-- Begin Jekyll SEO tag v2.5.0 -->
|
||||
<!-- Begin Jekyll SEO tag v2.6.1 -->
|
||||
<title>Troubleshooting | cellxgene</title>
|
||||
<meta name="generator" content="Jekyll v3.8.5" />
|
||||
<meta property="og:title" content="Troubleshooting" />
|
||||
@@ -16,10 +16,10 @@
|
||||
<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html" />
|
||||
<meta property="og:site_name" content="cellxgene" />
|
||||
<script type="application/ld+json">
|
||||
{"description":"Troubleshooting","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Troubleshooting","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","@context":"http://schema.org"}</script>
|
||||
{"publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"description":"Troubleshooting","@type":"WebPage","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","headline":"Troubleshooting","@context":"https://schema.org"}</script>
|
||||
<!-- End Jekyll SEO tag -->
|
||||
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=994a7b19bb6437b8e48d92683aab7fd8077477f7">
|
||||
<link rel="stylesheet" href="/cellxgene/assets/css/style.css?v=1e63ea908a47166f77f60b5d7c978a0e5dbe1d18">
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<![endif]-->
|
||||
|
||||
@@ -25,7 +25,7 @@ You should see your web browser open with the following
|
||||
You can also launch from a URL directly like this:
|
||||
|
||||
```
|
||||
cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
|
||||
cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/example-dataset/pbmc3k.h5ad
|
||||
```
|
||||
|
||||
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:
|
||||
|
||||
@@ -17,7 +17,7 @@ cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in `
|
||||
## Differential expression
|
||||
|
||||
We're actively working on how to improve differential expression within the app.
|
||||
**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/master/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
|
||||
**N.B.: the [current implementation](https://github.com/chanzuckerberg/cellxgene/blob/main/server/app/scanpy_engine/diffexp.py#L40) assumes normally distributed values on a linear scale.**
|
||||
|
||||
Currently, we use a [Welch's _t_-test](https://en.wikipedia.org/wiki/Welch%27s_t-test), which assumes that the two populations are each normally distributed, but may have unequal variance. We use a two-sided t-test against the null hypothesis that the two populations have **equal** means. P-values are adjusted with the [Bonferroni corrrection](https://en.wikipedia.org/wiki/Bonferroni_correction).
|
||||
|
||||
|
||||
Reference in New Issue
Block a user