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

[Tim Triche, Jr.]

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