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noamteyssier / adpbulk

pseudobulking on an AnnData object
MIT License
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Does adpbulk normalize for the number of cells per cluster #3

Closed abhay1109 closed 1 year ago

abhay1109 commented 1 year ago

Hi,

Thank you for publishing this package. I am using it to pseudobulk based on cluster annotations in scanpy. However, I'm still not sure how this package works. Does it simply add up the count values of all the cells in each cluster or does it subsample equal number of cells from each cluster?

Best, Abhay

noamteyssier commented 1 year ago

Hey Abhay,

it simply adds up the count values (or takes the mean) of all the cell-transcripts in each cluster.

It doesn't subsample equal numbers of cells from each cluster.