hello friends I am a PhD student and I have little time to finish my studies and defend my thesis. I have to pay a heavy financial penalty for every day of delay in defense. During my work, my supervisor did not help me and now I have data that needs to be analyzed. Of course, I have advanced the data to differential expression analysis, but my friend who was helping me is very busy now. Now I want to ask, is there anyone who can answer my questions? As the first question, how can I determine and count up and down genes in the results of EdgeR?

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Is this quesion related to your earlier question? RNAseq analysis

If you've already done an edgeR analysis, you can easily count up and down genes by:

summary(decideTests(results))

and you can see which genes are DE by

topTags(results)

Help is available from the edgeR User's Guide or from the edgeRQL workflow: https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html