Incorrect reference for `score_genes` in documentation

[mbernste]

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• [X] I have checked that this issue has not already been reported.
• [X] I have confirmed this bug exists on the latest version of scanpy.
• [X] (optional) I have confirmed this bug exists on the master branch of scanpy.

What happened?

I believe that the reference for the score_genes function is incorrect. It looks to be listed as Satija et al. (2015), which is this paper: https://doi.org/10.1038/nbt.3192

If I am not mistaken the correct reference is this paper: DOI: 10.1126/science.aad0501

Minimal code sample

N/A

Error output

No response

Versions

N/A

[dawe]

Hello, I'm a bit confused. Satija 2015 references Seurat v1, but I'm not sure the function was already implemented. When I ported the first version into scanpy, Seurat v2 was already out, the proper reference should then be Butler 2018

[mbernste]

I believe that this scoring algorithm was implemented in Seurat, but it looks to be originally devised in Tirosh et al. (2016) cited above. Here is the documentation for the corresponding function in Seurat, which cites Tirosh et al: https://satijalab.org/seurat/reference/addmodulescore

[flying-sheep]

the reference system works well now, so PRs to fix it are welcome!

[MLubetzki]

Tirosh 2016 looks right to me, they explain it in the Materials and Methods under "MITF and AXL expression programs and cell scores". I just submitted a PR that fixes this.