On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer <[email protected] > wrote:
> and in which package is it implemented? > > The easiest place is in the chipseq package vignette. Just copy/paste and adapt that code. > > On Mon, Mar 1, 2010 at 2:39 PM, Michael Lawrence < > [email protected]> wrote: > >> >> >> On Mon, Mar 1, 2010 at 5:25 AM, Martin Morgan <[email protected]> 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 >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >> >> > > > -- > Johannes Rainer, PhD > Bioinformatics Group, > Division Molecular Pathophysiology, > Biocenter, Medical University Innsbruck, > Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria > and > Tyrolean Cancer Research Institute > Innrain 66, 6020 Innsbruck, Austria > > Tel.: +43 512 570485 13 > Email: [email protected] > [email protected] > URL: http://bioinfo.i-med.ac.at > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
