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neurorestore / DE-analysis

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Unknown test: mixed_lm #5

Open Nayrouz109 opened 1 year ago

Nayrouz109 commented 1 year ago

Hello,

Thank you for providing the code, it's been really helpful.

I have a question about the seurat_DE function in the DE-analysis/R/functions/run_DE.R, specifying de_test = mixed_lm results in an error (Unknown test: mixed_lm).

So I am wondering, does FindMarkers(test.use = "mixed_lm") work?

Thanks!

skinnider commented 1 year ago

The code in this repository requires a custom build of Seurat that has been modified to add additional DE methods, return test statistics in addition to p-values, and other functionality - cf. the Methods section of the Nat. Commun. paper:

The modified version of Seurat 3.1.5 used to perform all single-cell DE analyses reported in this study is available from http://github.com/jordansquair/Seurat.