Is there a command line protocol for looking doing ontology/pathway analysis (i.e. not through DAVID or PANTHER)? How do the Pros do it?

Question

[Daniel]

Using DAVID was what I was taught all those years ago, but it just seems so primitive and awkward when I have to pull gene lists down from the cluster and upload to a site. The same with PANTHER which I've more recently found.

How do people normally do this kind of analysis? Is there a package, or protocol that people who do this regularly can point to? I'm wondering if there's something akin to the tophat/cufflinks nature protocol paper that lays the basic steps out. Something which ends with files listing ontologies/pathways/functions with up and down regulations and stats?

Thanks

[Endre Bakken Stovner]

https://github.com/endrebak/goverlap

Answer 1

[dago]

In Bioconductor there are many packages that can do that, something like topGO or others.

You can look at this answer.