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carmonalab / UCell

Gene set scoring for single-cell data
GNU General Public License v3.0
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Applying UCell on RNA or SCT assay? #34

Closed balzasch closed 8 months ago

balzasch commented 8 months ago

Hi,

thanks for providing this very useful and easy-to-apply package! I was wondering whether you recommend to run AddModuleScore_UCell() on the "SCT" or "RNA" assay? Thanks!

mass-a commented 8 months ago

Hello, in principle it shouldn't matter which assay you use.

UCell scores are calculated individually for each cell and are only based on the relative gene ranks. As long as the normalization does not alter the rank of the genes, the resulting score should be identical. In fact, you could also just calculate UCell scores directly on the count matrix with the same results.

-m