Hey guys,

I'm wondering if anyone has given any thought to some sort of generic
framework for chipseq analysis in Bioconductor, based on the IRanges,
Biostrings, etc infrastructure. chipseq has some nice utilities; could it be
transformed into some sort of generic chipseq pipeline? Something like how
the 'affy' package (I think?) allows other packages to provide alternative
implementations for particular stages. Just having a clean, refined,
approximately complete set of chipseq-focused utilities would be nice.
Presumably chipseq could fill that role? I think we now have a good idea of
the basic steps in chipseq analysis, so it's probably time for such a
package to emerge.

Comments?

Michael

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