Hello, I'm analyzing some RNA-Seq data using DESeq2 and have a couple of questions on how to set up my experimental design.

My experimental design has a control ("ctrl") and three treatments ("treat1", "treat2" and "treat3"). I want to see if there is an expression differences of these treatments compared to control.

Could anybody help me to write the contrast code? Also, can I run all the comparisons together or each treatment have to be compared separately to control?

res <- results(dds, contrast=c("treatment","ctrl","treat1",....))???

Thank you!

"Could anybody help me to write the contrast code? "

Writing contrast code for your analysis is up to you, there are vignettes and help pages and workflows you should read before posting to the support site. (Start with DESeq2 vignette and the workflow is linked from the first page).

"can I run all the comparisons together"

No.