winging it here tim > select(Homo.sapiens, keys="ENSG00000198727", keytype="ENSEMBL", columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1 mapping between keys and columns ENSEMBL GENENAME SYMBOL CDSCHROM GENEID 1 ENSG00000198727 cytochrome b CYTB <NA> 4519 > select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL", columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1 mapping between keys and columns SYMBOL GENENAME CDSCHROM GENEID 1 MTCYBP1 MT-CYB pseudogene 1 <NA> 100499418
relevant? On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. <tim.tri...@gmail.com> wrote: > Hi Lori and fellow maintainers, > > I had a strange experience yesterday where I pulled down genes and > transcripts from Homo.sapiens, only to discover that all mitochondrial > encoded genes (MT-CYB, MT-CO2, etc) were missing. > > Is there an historical reason why this is so? Obviously these transcripts > are physiologically important, but beyond that, they’re also used all the > time in single cell sequencing to estimate viability. > > Best, > > --t > > > On Mar 28, 2024, at 8:47 AM, Kern, Lori via Bioc-devel < > bioc-devel@r-project.org> wrote: > > > > Hello Bioconductor community, > > > > The newest db0, OrgDb, and TxDb annotation packages for the upcoming > Bioconductor 3.19 release are up and available for download in the devel > version of Bioconductor. > > > > The deadline for submitting contributed annotation packages will be > Wednesday April 17 th. > > > > The new db0 packages are: > > > > anopheles.db0_3.19.0.tar.gz > > arabidopsis.db0_3.19.0.tar.gz > > bovine.db0_3.19.0.tar.gz > > canine.db0_3.19.0.tar.gz > > chicken.db0_3.19.0.tar.gz > > chimp.db0_3.19.0.tar.gz > > ecoliK12.db0_3.19.0.tar.gz > > ecoliSakai.db0_3.19.0.tar.gz > > fly.db0_3.19.0.tar.gz > > human.db0_3.19.0.tar.gz > > malaria.db0_3.19.0.tar.gz > > mouse.db0_3.19.0.tar.gz > > pig.db0_3.19.0.tar.gz > > rat.db0_3.19.0.tar.gz > > rhesus.db0_3.19.0.tar.gz > > worm.db0_3.19.0.tar.gz > > xenopus.db0_3.19.0.tar.gz > > yeast.db0_3.19.0.tar.gz > > zebrafish.db0_3.19.0.tar.gz > > > > The new OrgDb packages are: > > > > GO.db_3.19.0.tar.gz > > org.Ag.eg.db_3.19.0.tar.gz > > org.At.tair.db_3.19.0.tar.gz > > org.Bt.eg.db_3.19.0.tar.gz > > org.Ce.eg.db_3.19.0.tar.gz > > org.Cf.eg.db_3.19.0.tar.gz > > org.Dm.eg.db_3.19.0.tar.gz > > org.Dr.eg.db_3.19.0.tar.gz > > org.EcK12.eg.db_3.19.0.tar.gz > > org.EcSakai.eg.db_3.19.0.tar.gz > > org.Gg.eg.db_3.19.0.tar.gz > > org.Hs.eg.db_3.19.0.tar.gz > > org.Mm.eg.db_3.19.0.tar.gz > > org.Mmu.eg.db_3.19.0.tar.gz > > org.Pt.eg.db_3.19.0.tar.gz > > org.Rn.eg.db_3.19.0.tar.gz > > org.Sc.eg.db_3.19.0.tar.gz > > org.Ss.eg.db_3.19.0.tar.gz > > org.Xl.eg.db_3.19.0.tar.gz > > Orthology.eg.db_3.19.0.tar.gz > > PFAM.db_3.19.0.tar.gz > > > > The new TxDb packages are: > > > > TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz > > TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz > > > > Thank you > > > > > > Lori Shepherd - Kern > > > > Bioconductor Core Team > > > > Roswell Park Comprehensive Cancer Center > > > > Department of Biostatistics & Bioinformatics > > > > Elm & Carlton Streets > > > > Buffalo, New York 14263 > > > > > > 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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this email is intended only for the p...{{dropped:15}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel