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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
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@@ -25,7 +25,7 @@ You should see your web browser open with the following
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You can also launch from a URL directly like this:
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```
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cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/master/example-dataset/pbmc3k.h5ad
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cellxgene launch https://github.com/chanzuckerberg/cellxgene/blob/main/example-dataset/pbmc3k.h5ad
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```
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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:
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@@ -17,7 +17,7 @@ cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in `
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## Differential expression
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We're actively working on how to improve differential expression within the app.
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**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.**
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**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.**
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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).
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