I am looking to do standardized Gene Ontology analysis based on a cutoff and Overrepresentation Analysis(ORA, not GSEA).
For this, I've been using gprofiler, etc.
But I need to do this in a standardized way where I can supply my own versioned .gmt files. In topGO, you have to use "their" GO files, and I don't like its over complicated object oriented design. Clusterprofiler was too "high level" for me and not really suitable for a professional study.
I'm looking for a simple package, like GAGE, except for ORA, where I supply -my gmt files -my DEGs -my background genes -pvalue cutoff -Method and other more specific parameters.
Is there a good package in bioconductor where I can do this?