[BioC] Ensembl or Gencode version of TxDb.Hsapiens.UCSC.hg19.knownGene

James W. MacDonald jmacdon at uw.edu
Fri Oct 18 15:27:22 CEST 2013

Hi Adai,

See makeTranscriptDbFromBiomart() in the GenomicFeatures package.



On Friday, October 18, 2013 9:18:46 AM, Adaikalavan Ramasamy wrote:
> Hi there,
> I am using the R package TxDb.Hsapiens.UCSC.hg19.knownGene to annotate SNPs
> using the locateVariants() function from the VariantAnnotation package.
> For reasons of compatibility with other pipelines I developed, I would like
> to use Ensembl/Gencode annotation. Is there a package for this? Otherwise
> please advice on how best to generate this myself.
> Thank you.
> Regards, Adai
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

More information about the Bioconductor mailing list