Hello, I'm learning about Gene Ontology analysis. I'm trying to understand the difference between the hyperGTest function from the GOstats package and the enrichGO function from the clusterProfiler package to determine which one I need to be using. If anyone can help me understand those two functions it would be really helpful.

Thank you

The main difference is that enrichGO fits a conventional hypergeometric test whereas hyperGTest allows you to do a conditional test as well. The conditional test is based on Adrian Alexa's paper.