Hi Ulrich, I was not sure about how much demand there is for the masked BSgenome packages in general so I was just waiting for someone to ask. Note that the masks are typically generated from data available at UCSC so it sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and BSgenome.Hsapiens.NCBI.hg38.masked available.
I'll prepare the 2 packages in the next couple of weeks and post back here when they are ready for download. Cheers, H. On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:
Hi, The latest human genome build GRCh38 has been around in Bioconductor for some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can tell, however, there is currently no package that provides easy access to masked/unmasked regions in the genome (like there is a .masked version that wraps BSgenome objects into MaskedBSgenome objects for many other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for hg19). Here is my question: does anybody have plans to include a package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name) into Bioconductor 3.1? At least I could not find anything in the current development branch. Thanks and best regards, Ulrich ------------------------------------------------------------------------ *Dr. Ulrich Bodenhofer* Associate Professor Institute of Bioinformatics *Johannes Kepler University* Altenberger Str. 69 4040 Linz, Austria Tel. +43 732 2468 4526 Fax +43 732 2468 4539 bodenho...@bioinf.jku.at <mailto:bodenho...@bioinf.jku.at> http://www.bioinf.jku.at/ <http://www.bioinf.jku.at> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
