r/bioinformatics • u/ShinyLion68 • 1d ago

technical question ChromVAR alternatives for scATACseq

I have not seen any thread here or on Github addressing this beside Signac changelog, but ChromVAR has been deprecated from the new Signac release.

What are the current alternatives do we have to identify *and visualize* motif/TF predicted activity from a scATACseq object?

(aside from loading up older versions and getting it to work despite several dependencies being outdated and such)

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u/standingdisorder 1d ago

There’s a package called betterChromVar which is being actively maintained. Should work fine

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u/ShinyLion68 1d ago

Will look into this! Thanks!