Hi, the people behind BayesPeak (http://www.biomedcentral.com/1471-2105/10/299) are also putting together a BioC package. I don't think it's out yet, but if you contact the authors of the article you can probably get a test version.
\Heidi > 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
