I think FindPeaks is one of the best ChIP-Seq packages currently available. Yes, I would like to have better documentation, yes there are occasionally bugs in it, and yes, the fact that I'm the only full-time developer on the project are detriments.... But those are only complaints, and they don't diminish the fact that I think FindPeaks can out peak-call, out control, out compare.... and will outlast, outwit and outplay all of it's opponents. (=
FindPeaks is actually a VERY well written piece of code, and has the flexibility to do SO much more than just ChIP-Seq. If I had my way, I'd have another developer or two working with the code to expand many of the really cool features that it already has.
If people are considering using it, I'm always happy to help get them started, and I'm thrilled to add more people to the project if they would like to contribute.
So, just to make things clear - I think FindPeaks (and the rest of the Vancouver Short Read Analysis Package) are great pieces of software, and are truly worth using. If you don't believe me, send me an email, and I'll help make you a believer too. (=