Seurat DESeq2 interaction terms
Wondering if there is a good tutorial out the for differential expression analysis using interaction terms in Seurat with DESeq2? Like for instance if having two genotypes and two treatment conditions? Thanks!
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LacquerHed •
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Do you have biological replicates that allow pseudobulk-DE or do you strictly want to use the per-cell counts? I would probably simply take the matrix of raw UMI counts out of Seurat and then do the DESeq2 part manually once it goes beyond a simple two-group comparison. DESeq2 should be much faster after the next version (1.30.0, see https://github.com/mikelove/DESeq2/blob/master/NEWS) is being released due to addition of a new method to estimate the model parameters (from the glmGamPoi package).
I do have biological replicates that allow pseudobulk-DE. Thanks for the suggestion.
If for instance I did not have replicates, how would you go about using the per-cell counts for more complex comparisons? Have the DESeq2 interaction part down, just wondering about other options. Thanks.