As stated in the title: I am looking for a rank-based (or possibly score-based, but I am not sure any such methods exist) tool for GO enrichment that can be used from R.
All the packages I have found so far (e.g. TopGO) only offer enrichment based on a selected set of genes (possibly obtained through testing). Tools such as GOrilla do it, but only as web-tools. This paper even gives a pretty long list (class II of table 2), but none appear to have an R interface.
Does anyone have experience getting rank-based GO enrichment scores in R?