thanks, I will have a look at that. bests, jo
On Mon, Mar 1, 2010 at 4:04 PM, Heidi Dvinge <[email protected]> wrote: > 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 > > > > > -- 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
