[Bioc-sig-seq] peak calling/detection algorithm available in Bioconductor?

[Heidi Dvinge]

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
> <johannes.rainer at 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 at gene.com>wrote:
>>
>>>
>>>
>>> On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer <
>>> johannes.rainer at 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 at gene.com> wrote:
>>>>
>>>>>
>>>>>
>>>>> On Mon, Mar 1, 2010 at 5:25 AM, Martin Morgan
>>>>> <mtmorgan at 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 at 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 at i-med.ac.at
>>>>            johannes.rainer at 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 at i-med.ac.at
>>           johannes.rainer at tcri.at
>> URL:   http://bioinfo.i-med.ac.at
>>
>>        [[alternative HTML version deleted]]
>>
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>> 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
>
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