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In function getDifferentialGenes currently supports only pagoda2. To fix it, we need to create function getDifferentialGenesSeurat and call it conditionally in the same way as getDifferentialGenesP2.
Function should have the same format (see getDifferentialGenesP2), but should call FindAllMarkers and ensure that dataframe with DE result has correct format (i.e. Z column with Z-score and gene names as rownames).
The text was updated successfully, but these errors were encountered:
Actually, it looks like FindAllMarkers in Seurat only works with clustering tree, which we lack in most clustering algorithms. Maybe it would be possible to write a wrapper around FindMarkers.default.
In function getDifferentialGenes currently supports only pagoda2. To fix it, we need to create function
getDifferentialGenesSeurat
and call it conditionally in the same way asgetDifferentialGenesP2
.Function should have the same format (see
getDifferentialGenesP2
), but should callFindAllMarkers
and ensure that dataframe with DE result has correct format (i.e.Z
column with Z-score and gene names as rownames).The text was updated successfully, but these errors were encountered: