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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/posts/methods.md
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@@ -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).