On Thu, Feb 12, 2009 at 1:18 AM, Ingunn Berget <ingunn.berget@umb.no> wrote:

> Are there any packages in Bioconductor for analysing RNA-seq data?
>

The short answer is no, nothing explicitly for RNA-seq. However, there's a
collection of tools for analyzing general high-throughput sequencing data.
ShortRead for preprocessing, Biostrings for sequence matching/alignment,
IRanges for manipulating interval data, rtracklayer for working with genomic
annotation data and interfacing with the UCSC genome browser, HilbertVisGUI
for visualization, and there's several more. One might anticipate that these
tools will soon evolve to address the specific RNA-seq use case.

Michael


>
> Ingunn Berget (Dr. Scient)
> UMB, box 5003, IHA
> 1432 Ås
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>
> Centre for Integrative Genetics, www.cigene.no
> Centre for Biospectroscopy and Data Modelling, www.specmod.org
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