Hi!

Currently UGENE uses cuffdiff for differential expression analysis. Cuffdiff is outdated and produces more false positives than many other tools. I think many people will be glad if you add a more modern tool for the differential expression analysis, for example DeSeq2. A comparison can be found in the paper "How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?" (2016).