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

[Steve Lianoglou]

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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>



-- 
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