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

Bhagwat, Aditya Ad|ty@@Bh@gw@t @end|ng |rom mp|-bn@mpg@de
Tue Oct 15 14:15:50 CEST 2019

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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