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ZJU-UoE-CCW-LAB / scCDC

single-cell Contamination Detection and Correction
GNU General Public License v3.0
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SCT #6

Open snglcl opened 2 months ago

snglcl commented 2 months ago

Hello, thanks for this tool. I was wondering if the contamination correction will still work if we normalized with SCTransform v2 instead of log norm/scale?

Stephen1202-Wang commented 2 months ago

Hi, Thank you for using our tools.

scCDC defines eGCG-/+ clusters based on normalized data and the default normalization method is log1pCP10k. If I understand correctly, the normalization method in SCTransform is log1p(counts). scCDC should be robust to various normalization methods, including SCTransform, but we have not yet validated these alternatives. It would be OK to use SCTransform but if there's no specific reason to do so, we recommend sticking with log1pCP10k for optimal results.