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Published 20 hours ago • verified publisher icon broadinstitute

Use with single-cell ATAC-Seq?

Open davidjohngreen opened this issue 4 years ago • 1 comments

Hi there,

Any ideas about whether ABC can be used with single-cell ATAC-seq data?

Best,

David Green

davidjohngreen avatar Dec 09 '20 23:12 davidjohngreen

Yes. I'd suggest using the sc-ATAC to create pseudobulk (with or without evening out reads per-cell) ATAC, and it should work similarly to using bulk ATAC.

thouis avatar Dec 10 '20 00:12 thouis

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

We have a section dedicated to scATAC-seq in the ReadTheDocs

atancoder avatar Dec 07 '23 23:12 atancoder