Hi, There's also the SPP package (not bioconductor, but still R):
http://compbio.med.harvard.edu/Supplements/ChIP-seq/ http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html -steve On Mon, Mar 1, 2010 at 9:50 AM, Johannes Rainer <[email protected]> wrote: > yes, the chipseq vignette is great, I've already adapted and used the code, > but as far as I understand the only way to identify peaks there is to use > some sort of cut-off (e.g. define islands with a lower of xx, or a x-fold > different coverage between sample to control). I'm interested in a way to > calculate a p-value for the "enrichment" of the peak, taking the nr of reads > and the depth into account. > > > On Mon, Mar 1, 2010 at 3:20 PM, Michael Lawrence > <[email protected]>wrote: > >> >> >> 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 >>> >>> >> > > > -- > 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 > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
