On Mon, Mar 1, 2010 at 5:25 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 03/01/2010 12:40 AM, Johannes Rainer wrote:
> > dear all,
> >
> > I'm just wondering if anybody has already implemented a ChIP-seq peak
> > detection algorithm (like MACS, PeakSeq...) or plans to do so.
>
> See http://bioconductor.org/packages/release/Software.html and search
> for chipseq, e.g., chipseq, ChIPseqR implement peak detection algorithms
> (though not MACS or PeakSeq; approximations of these algorithms are not
> difficult to implement using IRanges / Biostrings / ShortRead
> infrastructure).
>
>
Just to clarify, the chipseq package, while useful for chipseq in general,
does not implement a peak detection method. Deepayan's method is implemented
separately.


> Martin
>
> >
> > bests, jo
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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