Regressing out variables in pearson residual normalization

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1

Hello!

I was looking into normalizing my single cell data using the Pearson Residual method in the experimental API. However, previously I regressed out mitochondrial & cell cycle differences in Seurat with SCTransform (it was a paramter within SCTransform). I was wondering in the case of Pearson Residuals, is it possible to perform the regression on the normalized Pearson Residuals?

Thank you!

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2

I am also curious about this especially since the output of the Pearson Residual normalisation is still very easy to separate with PCA when looking at just the cell cycle genes.

3

Follow up on this, is there an actionable workflow for apply regress_out() in Pearson residual normalization in scanpy?