On Mon, Mar 1, 2010 at 6:53 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> 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
> <johannes.rainer@i-med.ac.at> 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
> > <lawrence.michael@gene.com>wrote:
> >
> >>
> >>
> >> On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer <
> >> johannes.rainer@i-med.ac.at> 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 <
> >>> lawrence.michael@gene.com> wrote:
> >>>
> >>>>
> >>>>
> >>>> On Mon, Mar 1, 2010 at 5:25 AM, Martin Morgan <mtmorgan@fhcrc.org
> >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
> >>>>> Bioc-sig-sequencing@r-project.org
> >>>>> 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:  johannes.rainer@i-med.ac.at
> >>>            johannes.rainer@tcri.at
> >>> 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:  johannes.rainer@i-med.ac.at
> >           johannes.rainer@tcri.at
> > URL:   http://bioinfo.i-med.ac.at
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > 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>
>

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