Hi all, I'm using R 2.10-devel w/ BioC 2.5 because I want to get a bit more acquainted w/ the nextgenseq packages. I noticed, however, that the BSgenome.Hsapiens.UCSC.hg19 package isn't in the BioC 2.5 Annotation downloads: http://www.bioconductor.org/packages/2.5/data/annotation/ Is there a particular reason for that besides not having gotten around to it? Can I simply d/l the *.hg19 source package from BioC 2.4 and compile it myself for R 2.10? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi Steve, Steve Lianoglou wrote: > Hi all, > > I'm using R 2.10-devel w/ BioC 2.5 because I want to get a bit more > acquainted w/ the nextgenseq packages. I noticed, however, that the > BSgenome.Hsapiens.UCSC.hg19 package isn't in the BioC 2.5 Annotation > downloads: > > http://www.bioconductor.org/packages/2.5/data/annotation/ > > Is there a particular reason for that besides not having gotten around > to it? No particular reason. > > Can I simply d/l the *.hg19 source package from BioC 2.4 and compile it > myself for R 2.10? Yes, that should work. Some upcoming changes in the underlying containers that are used to store the chromosome sequences might break backward compatibility for those BSgenome data packages between BioC 2.4 and 2.5 but for now they are compatible. H. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319