On Mon, Mar 1, 2010 at 6:53 AM, Steve Lianoglou < [email protected]> wrote:
> 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 > > It's unfortunate that those guys have decided to reimplement much of what is already available in Bioconductor. In particular, they could probably use ShortRead for their I/O. > -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<http://cbio.mskcc.org/%7Elianos/contact> > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
