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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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Run after data integration #8

Open YasuhiroOnogi opened 1 month ago

YasuhiroOnogi commented 1 month ago

Hello. This tool seems very useful. To run this for multiple samples integrated into one object, which way (harmony, seurat integration etc,) are compatible and which is the first should be done, data integration or scCDC?

Stephen1202-Wang commented 1 month ago

Hi @YasuhiroOnogi ,

Thanks for using our tool. scCDC assumes that contamination is sample-specific, meaning that the contamination can vary across samples sequenced in different batches. Since scCDC performs decontamination in a sample-specific and cell type-specific manner, we recommend conducting the decontamination process with scCDC first.

YasuhiroOnogi commented 1 month ago

Thank you, Weijian, for your kind guidance. I will run this first, then do a batch correction.

cystone commented 6 days ago

The tool is very cThe tool is really cool. I was wondering, could you introduce parameters to also run on multiple Seurat V4 objects, just like the scDblFinder function does? Thank you!

library(BiocParallel) library(scDblFinder) sce <- scDblFinder(sce, samples="sample_id", BPPARAM=MulticoreParam(3))

Stephen1202-Wang commented 6 days ago

Hi @cystone, Thanks for your suggestion. We'll review it and explore the possibility of enabling scCDC to run on multiple objects.