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?