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Add support for Seurat findMarkerGenes #16

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VPetukhov opened this issue Apr 10, 2019 · 1 comment
Open

Add support for Seurat findMarkerGenes #16

VPetukhov opened this issue Apr 10, 2019 · 1 comment
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enhancement New feature or request help wanted Extra attention is needed

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@VPetukhov
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VPetukhov commented Apr 10, 2019

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).

@VPetukhov
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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.

@evanbiederstedt evanbiederstedt added the enhancement New feature or request label Jul 2, 2020
@evanbiederstedt evanbiederstedt added the help wanted Extra attention is needed label Sep 11, 2020
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