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

[Tim Triche, Jr.]

yep, looks like that's the problem

I wonder why it doesn't have a CDS chromosome in ENSEMBL?  That's a bit
nuts.

It is indeed indexed to MT in the canonical ENSEMBL database:
https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000198727;r=MT:14747-15887;t=ENST00000361789


--t


On Thu, Mar 28, 2024 at 9:59 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> 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
>> >
>> >
>> > 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 using r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> The information in this email is intended only for the...{{dropped:11}}