Are there any packages in Bioconductor for analysing RNA-seq data? Ingunn Berget (Dr. Scient) UMB, box 5003, IHA 1432 ?s Norway Centre for Integrative Genetics, www.cigene.no Centre for Biospectroscopy and Data Modelling, www.specmod.org

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 > Norway > > Centre for Integrative Genetics, www.cigene.no > Centre for Biospectroscopy and Data Modelling, www.specmod.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]