[Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

[Vincent Carey]

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.triche using 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 using 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
> >
> >
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