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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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Use with single-cell ATAC-Seq? #46

Closed davidjohngreen closed 11 months ago

davidjohngreen commented 3 years ago

Hi there,

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

Best,

David Green

thouis commented 3 years ago

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.

atancoder commented 11 months ago

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