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: [email protected] http://www.pri.wur.nl > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of Johannes Rainer > Sent: maandag 1 maart 2010 9:40 > To: [email protected] > 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: [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 > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
