filtered export from ArchR + Seurat scRNA?

welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets

GNU General Public License v3.0

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filtered export from ArchR + Seurat scRNA? #197

Closed wfma closed 7 months ago

wfma commented 4 years ago

Hi! I have a technical question. I have a set of scRNA that has been processed and labeled in Seurat and I wish to use that data to identify a set of scATAC-seq that have been processed in ArchR.

It seems that I can export scATAC data from ArchR via getMatrixFromProject that export a SummarizedExperiment obj. I am not sure the best way to create a liger obj is with these two starting objs. Can you help? Thanks, Wei

wfma commented 4 years ago

Hello- just to follow up with more information; it seems that archR already calculates and exports a gene-score analogous to a count matrix in scRNA-seq. It seems I can just bypass the bedmap counting step, but I am not sure where and how I should go about creating the liger obj.