Question

Multi-group DE scRNA-seq comps without replicates

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3.5 years ago

LacquerHed ▴ 30

Wondering if its possible to do multi-group DE comparisons of 10X/Seurat data without replicates, using perhaps just the per-cell counts alone? To compare DE genes across clusters from lets say 2 genotypes and 2 treatments.Thanks.

seurat RNA-Seq scRNA-seq DESeq2 • 775 views

ADD COMMENT • link updated 3.5 years ago by khorms ▴ 230 • written 3.5 years ago by LacquerHed ▴ 30

score 1 · Answer 1 · 2020-10-27

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3.5 years ago

khorms ▴ 230

Yes there are definitely methods for DE comparisons implemented in the commonly used single cell packages; for example, see this discussion (link) for scanpy

ADD COMMENT • link 3.5 years ago by khorms ▴ 230

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Do you know of any good tutorials for doing this in Seurat? Thanks.

ADD REPLY • link 3.5 years ago by LacquerHed ▴ 30