[BioC] RIP/CLIP-seq

[Martin Morgan]

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
>
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