I would like to analyze differential transcript usage (DTU)/Isoform switching following Salmon quantification, but have a fairly complex three-way factorial design. I am interested in three factors: Genotype (mutant, WT), Sex (M, F) and Age (1D, 28D). I am not only interested in some simple contrasts, but also in some interaction contrasts (e.g. Genotype by Sex and Genotype by Age). I used edgeR for DE analysis and was able to pretty easily set up the appropriate contrasts, but, at least from my understanding, edgeR is not really set up to perform DTU analysis. I would ideally like to do something similar for DTU rather than performing all pairwise comparisons separately and not really being able to look at interactions. However, I am getting stuck finding an analysis pipeline that would work with this complex design. I've considered DEXSeq and IsoformSwitchAnalyzeR but it is not clear to me from the documentation how to set up the contrasts I would be interested in (it seems like maybe it's possible but I'm not sure). I would greatly appreciate any advice on whether these or other packages would work for this design, or whether pairwise comparisons would be the best way to go. Thank you in advance for any advice!