Congena (Co-expressed gene-set enrichment analysis) Input?

Question

[omargmc.tak]

Hello, I'm starting to use COGENA (Co-expressed gene-set enrichment analysis) but I'm not sure what format my differential expression analysis should have. I use DEseq2 for DE analysis and I have a count table. What format that I give to COGENA to start the analysis? Thank you in advance.

[rpolicastro]

It's not immediately clear in their documentation, but I believe it uses a count matrix (genes as rows and samples as column) of raw counts with only DEGs retained, and a vector that specifies which group each sample corresponds to. You should double check though that it's raw and not normalized counts it wants though.