, March 28, 2024 8:47 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available
Hello Bioconductor community,
The newest db0, OrgDb, and TxDb annotation packages for the upcoming
Bioconductor 3.19 release are up and available for download
+ |252881 ENST0386347.1
>---
>seqinfo: 439 sequences (1 circular) from an unspecified genome; no
> seqlengths
>
>
> As with most human endeavors, the weight of history hangs heavy on
> Bioconductor, and it’s often easier to understand h
imes to get affy removed in lieu of oligo, to no avail.
From: Tim Triche, Jr.
Sent: Thursday, March 28, 2024 10:40 AM
To: James W. MacDonald
Cc: Vincent Carey ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
is this an argument in favor
hg38 genome
>
> Everything is mapped via the GENEID, and if you query the UCSC genome
> browser for hg38/knownGene, asking for gene name, known gene ID and gene
> symbol, you will get the first and last but not the middle.
>
>
>
> -----Original Message-
> From: Bioc-devel
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=ENSG0198727;r=MT:14747-15887;t=ENST0361789
--t
On Thu,
m Triche, Jr.
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
winging it here tim
> select(Homo.sapiens, keys="ENSG0198727", keytype="ENSEMBL",
columns=c("GENENAME", "GENEID", "CDSCHROM&q
winging it here tim
> select(Homo.sapiens, keys="ENSG0198727", keytype="ENSEMBL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
1 ENSG0198727 cytochrome b CYTB
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
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
