I was running kegga and goana as follows:
> kegga.de=kegga(lrt, species="Mm") > go <- goana(lrt, species= 'Mm') > v <- topGO(go, n=100)
For both, the output is a list of pathways that show a number of upregulated, downregulated, or unchanged genes. See below:
Is there any simple way to visualize which of the genes are actually up or down in these pathways? I have previously used the Desktop version of GSEA by the Broad Institute, which allows nice visualization of these things.