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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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sub-typing function #236

Closed archieandrews10 closed 7 months ago

archieandrews10 commented 7 months ago

Hi Kai:

I was able to integrate snATACseq and snRNAseq data successfully. I transferred the cell type information from the RNAseq data to the snATACseq data. Using my marker genes, can I further sub-type the cells with any of the SnapATAC2's built-in functions? If yes, could you point me in that direction?

Thanks Avinash

archieandrews10 commented 7 months ago

Hi Kai, Any help on this? I predicted the C_scANVI subtype after integrating the scRNAseq. But I want to further subtype the cell that are under C_scANVI based on certain marker genes. I am unable to do using SnapATAC2. Is there a function that I can use?

kaizhang commented 7 months ago

There's no built-in function to do exactly this in SnapATAC2. But you can check with other tools that are designed specifically to analyze transcriptome dataset, e.g., scanpy.