Hello everyone! I have recently started to analyze RNA-seq data and I would like to know which tools are current now for the purpose of GO enrichment. I have checked out topGO, BiNGO, and building my own hypergeometric test, but none really satisfied me.
I am looking for suggestions of tools that do Gene Ontology Enrichment over a set of genes. I would like the tool to be able to receive a custom annotation and ontology, that enriches using the hypergeometric test and that does multiple test correction, FDR if possible. Any ideas of tools I haven't thought about?
Edit: topGO didn't really work for me as it doesn't work properly, and it made me create my own annotation packages. Also it lacked hypergeometric test, which is the test I think is the most suitable for my experiment. topGO was also lacking multiple test correction and the documentation was not good at all.
BiNGO worked perfectly, however it doesn't have a way to automate it, and I need that in order to integrate the tool in a pipeline.
