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

[Muino, Jose]

Hi,

I think that several packages for CHIP-seq analysis will be submitted
soon to bioconductor. Of special interest could be PICS (
http://www.rglab.org/pics-and-bioconductor/ )

CSAR is the R package that I designed for the analysis of plant (this
is, small genome size) ChIP-seq experiments. When you are working with
big genomes, CSAR will need too RAM memory. In the coming days, I will
actualize the CSAR package with a new version, so the Ram requirements
will be below 1Gb even working with the mouse genome.

Dr. Jose M Muino
Plant Research International B.V.
Droevendaalsesteeg 1
P.O. Box 16, 6700 AA Wageningen, The Netherlands
Phone: +0317-481122.
E-mail: jose.muino at wur.nl
http://www.pri.wur.nl 
 

> -----Original Message-----
> From: bioc-sig-sequencing-bounces at r-project.org 
> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf 
> Of Johannes Rainer
> Sent: maandag 1 maart 2010 9:40
> To: bioc-sig-sequencing at r-project.org
> Subject: [Bioc-sig-seq] peak calling/detection algorithm 
> available inBioconductor?
> 
> 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.
> 
> bests, jo
> 
> --
> 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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