Hi,
Sorry in advance if the question is too "newbie " : I have 3 data sets :

1. 8000 genes
2. From this 8000 i have 200 that were found significant for a specific disease im analyzing .
3. Another data set with genes associated with another disease . I want to preform gene enrichment analysis with this 3 data frames and as I understand a test that uses hyper geometric distribution is appropriate here.
   I tried to use GofuncR but it doesn't have the option to use 3 data sets . Is there any other package that can preform this type of analysis .  Thanks