[Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Oct 15 14:22:09 CEST 2019

Again we would not recommend posting these types of questions to both the mailing list and the support site.
Since this is not a developer question -  the support site was the appropriate place -

We have members of the team working on developing the new TxDbs for the release and will look into the reasoning and post on the support site thread.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Bhagwat, Aditya <Aditya.Bhagwat using mpi-bn.mpg.de>
Sent: Tuesday, October 15, 2019 8:15 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

Dear BioC devel,

I want to convert geneids to GRanges by doing:

Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
        txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
        GenomicFeatures::genes(txdb)[c('100009600', '99889', '99982')]

        txdb <- TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
        GenomicFeatures::genes(txdb)[c('ENSMUSG00000000001', 'ENSMUSG00000000003')]

For human, hower, ensembl-centric TxDbs seem to be missing:
        txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
        GenomicFeatures::genes(txdb)[c('1', '10', '100')]

       # No TxDb.Hsapiens.UCSC.hg38.ensGene::TxDb.Hsapiens.UCSC.hg38.ensGene

Has this been a (perhaps recent) design choice to no longer offer the ensemble-centric TxDbs?

(The larger context of this question is the development of multicrispr (https://gitlab.gwdg.de/loosolab/software/multicrispr))

Thankyou for feedback!


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