[Bioc-sig-seq] [BioC] analysis ChIP-seq data
Martin Morgan
mtmorgan at fhcrc.org
Tue Jun 10 20:40:53 CEST 2008
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
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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