I am trying to catch up with the latest development in the gene set enrichment analysis and I am looking for recommendations describing practices and approaches that I might have missed. Perhaps older methods are still the best.
Here is the question:
Suppose you ran an analysis pipeline that produced a set of genes or transcripts (for example a set of differentially expressed transcripts across two conditions)
What is the tool or methodology of your choice to help you make sense of the role and function of your set?