May I know the currently widely used tools for GO enrichment analysis? I have some experience in GOseq, topGO, GOstat and Ontologizer, but I am not sure which one would you prefer?
There are many reasons to choose one over another tool, such as adjusting for gene length using GOseq and accounting for parent-child relationship using Ontologizer. It seems that the results from these different approaches are quite different, and no single tool can account for everything.
Thanks for sharing your experience on the selection of GO tools :)