[BioC] Trying to use BSgenome.Hsapiens.NCBI.GRCh38

Hervé Pagès hpages at fhcrc.org
Mon Apr 7 08:18:57 CEST 2014

Hi Hector,

I'm cc'ing the Bioconductor mailing list. Hope you don't mind.

On 04/04/2014 04:22 PM, Hector Zenil wrote:
> Hi Hervé
> I have installed, the latest versions of R and BiConductor and clite,
> etc. But BSgenome.Hsapiens.NCBI.GRCh38 doesn't come in the available
> genomes. Is there anything special I should be doing to have access to
> it?

It's only available in BioC devel and as a source package for now.
So if you are on Windows or Mac you need to use type="source" when
you do available.genomes() or biocLite(). For example on a Mac with
R 3.1.0:

   > library(BSgenome)

   > grep("GRCh38", available.genomes(), value=TRUE)

   > grep("GRCh38", available.genomes(type="source"), value=TRUE)
   [1] "BSgenome.Hsapiens.NCBI.GRCh38"

Note that in BioC devel, there is a new utility, getBSgenome(),
documented in the same man page as available.genomes(), that is
the recommended way to lookup a BSgenome object by genome assembly
or by full BSgenome package name. If the BSgenome package is not
installed, it will tell you exactly how to install it:

   > getBSgenome("GRCh38")
   Error in .stopOnAvailablePkg(genome, is.source = TRUE) :
     BSgenome.Hsapiens.NCBI.GRCh38 package is not currently installed.
     You first need to install it, which you can do with:
         biocLite("BSgenome.Hsapiens.NCBI.GRCh38", type="source")

See ?getBSgenome for the details.


> Thanks and best regards,
> - Hector
> Dr. Hector Zenil
> http://www.algorithmicnaturelab.org/hector.zenil
> Unit of Computational Medicine
> Karolinska Institute, Stockholm

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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