Thankyou Lori, Cheers,
Aditya ________________________________ From: Shepherd, Lori [lori.sheph...@roswellpark.org] Sent: Tuesday, October 15, 2019 2:22 PM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: Converting gene ids to GRanges - ensembl centric TxDb missing for human 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 - https://support.bioconductor.org/p/125609/ 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-boun...@r-project.org> on behalf of Bhagwat, Aditya <aditya.bhag...@mpi-bn.mpg.de> Sent: Tuesday, October 15, 2019 8:15 AM To: bioc-devel@r-project.org <bioc-devel@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: GenomicFeatures::genes(txdb)[geneids] 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! Aditya [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
