Rank-based GO enrichment packages for R?

Question

[Dave]

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?

Answer 1

[Ido Tamir]

https://www.bioconductor.org/packages/release/bioc/html/GSEABase.html

https://www.bioconductor.org/packages/release/BiocViews.html#___GeneSetEnrichment

[Dave]

Thanks for trying to answer, but I am afraid you did not really understand the question:

As I wrote, I am aware of the many R packages to do GO enrichment. The problem is that all the ones I have found so far (and indeed, the one you linked) are for gene set enrichment. They require you to specify a set of interest, to compare with the full set.

I am looking for a package that implements one of the existing method to work on ranked list, where no set is specified.

[Ido Tamir]

From your own link, where you wanted class 2 and "none appear to have an R interface"

"Class II: gene set enrichment analysis (GSEA)" GSEABase is what you wanted in the question.