[BioC] analysis ChIP-seq data

[Martin Morgan]

Hi Bodan --

"Bogdan Tanasa" <tanasa at gmail.com> writes:

> Hi everyone,
>
> I am in the process of analyzing a lot of ChIP-seq data and I am writing to ask
> if an analysis module becomes available for R/Bioconductor anytime soon.

Visit the bioc-sig-sequencing news group (Cc'd in the reply)

https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing

Current packages include Biostrings (for lots of string matching /
manipulation facilities) BSgenome (reference sequences, including
masked and SNP-injected versions) and ShortRead (for IO from ELAND or
MAQ, for instance, plus additional sorting, counting, and qa-related
functionality. There are posts in the bioc-sig-sequencing news group
about package use.

Maybe others will reply (to bioc-sig-sequencing) with additional
developments; I know people are working with and developing packages
for this data in R.

Martin

> Any information would be greatly appreciated. Thanks and best regards.
>
> Bogdan
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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