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neurorestore / Libra

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Can we speed up run_de with mixed models ? #34

Closed Nayrouz109 closed 1 year ago

Nayrouz109 commented 1 year ago

Hello,

Quick question, is it normal for run_DE(sc, de_family = "mixedmodel") to take too long to run (around 24hrs) when using one of your 18 gold standard single-cell datasets.

If so, is there a way you'd recommend using to speed it up?

Thanks!

skinnider commented 1 year ago

Short answer is this is normal and we did not find a way to speed it up using this particular implementation. You might be interested in NEBULA (https://www.nature.com/articles/s42003-021-02146-6) which seems like a promising alternative.

Nayrouz109 commented 1 year ago

ah thank you !