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Change default branch from 'master' to 'main' (#1589)

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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
2020-06-25 14:04:30 -07:00
committed by GitHub
parent 0fd3d4b8f4
commit 152c07a28e
25 changed files with 63 additions and 62 deletions
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docs/_site/posts/methods.html
+4 -4
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@@ -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>Methods | cellxgene</title>
<meta name="generator" content="Jekyll v3.8.5" />
<meta property="og:title" content="Methods" />
@@ -16,10 +16,10 @@
<meta property="og:url" content="https://chanzuckerberg.github.io/cellxgene/posts/methods.html" />
<meta property="og:site_name" content="cellxgene" />
<script type="application/ld+json">
{"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>
{"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>
<!-- 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]-->
@@ -114,7 +114,7 @@
<h2 id="differential-expression">Differential expression</h2>
<p>We’re actively working on how to improve differential expression within the app.
<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>
<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>