Thank you all for your reply. I also thought of using ChIP-seq tools, but was not sure they will work well since they all were designed for genome-wide rather than transcriptome-wide analysis. Mali On Tue, Aug 23, 2011 at 2:34 AM, Mercier Eloi <emercier@chibi.ubc.ca> wrote: > ** > Hi, > > I just want to mention that we developed a pipeline for ChIP-seq analysis > including : > *PICS for peak calling, > *rGADEM for *de novo* motif finding, > *and MotIV for PWMs manipulation and identification. > I think that it can be easily tweaked for CLiP-seq as mentioned by Martin. > These three packages are currently available in Bioconductor. > > Eloi > > > On 11-08-20 07:14 PM, Martin Morgan wrote: > > On 08/18/2011 06:02 AM, mali salmon wrote: > > Hi All > Does anyone know of a package to help with the analysis of RIP-seq and/or > CLIP-seq data? > > > Hi Mali -- No direct experience on my part and I don't think there's a > CLIP-seq package per se, but it sounds like the basic tools of ChIP- seq -- > ShortReadQ or perhaps DNAStringSet from Biostrings and the IRanges > infrastructure for pre-processing, alignment using a third-party tool (or > perhaps Biostrings::matchPDict), GappedAlignments for representing aligned > reads, coverage and slice for identifying enriched regions, maybe GRanges, > GenomicFeatures, ChIPpeakAnno for annotation -- would be useful here. There > are some approaches to peak calling in the chipseq package, including its > vignette. I'm not sure about general-purpose MEME finding within > Bioconductor, though there are position weight matricies in Biostrings. Hope > that's helpful without being to vague or misleading. > > Martin > > > Thanks > Mali > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > Eloi Mercier > Bioinformatics PhD Student, UBC > Paul Pavlidis Lab > 2185 East Mall > University of British Columbia > Vancouver BC V6T1Z4 > > [[alternative HTML version deleted]]