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carmonalab / UCell

Gene set scoring for single-cell data
GNU General Public License v3.0
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Is making UCell Scores of Single Genes Recommended? #5

Closed ksaunders73 closed 3 years ago

ksaunders73 commented 3 years ago

Hello!

I am using UCell to plot signatures onto my Seurat object. Is it okay to do this if there is only one gene in the signature? I asked this question except for AddModuleScore() to the Seurat developers, and they said just use their function FeaturePlot() (https://github.com/satijalab/seurat/issues/4904). I was not sure if the same applied to UCell scores or not.

Thanks for reading!

mass-a commented 3 years ago

Hello, in principle it's ok to calculate UCell scores with single-gene signatures. The score will correspond to the relative ranking of that gene compared to all other genes for a given cell. Using the FeaturePlot() directly on the expression data will visualize the absolute expression level for that gene. Both approaches are fine.

ksaunders73 commented 3 years ago

That makes sense, thank you very much!