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hms-dbmi / dseqr

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
https://docs.dseqr.com
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use group aware filterByExpr #163

Closed alexvpickering closed 4 years ago

alexvpickering commented 4 years ago

Without using group argument in edgeR::filterByExpr can get inappropriate filtering. For example ACE2 get's filtered in GSE147507 as it is only expressed in one of the cell types tested. This behaviour is resolved in filtering is delayed until after groups have been annotated.