Hi,
I am not part of the core Bioconductor team, but I have been in this
situation before. I would suggest you use the BFG Repo Cleaner (
https://rtyley.github.io/bfg-repo-cleaner/) to remove the errant bam file
from your repo's history. It's very likely that adding and removing the bam
file means
Hi!
This is my first message to the mailing list so apologies if I am breaking any
guidelines.
I am submitting a package called Ribostan and the build report gives an error
that the package tarball exceeds the size requirement. I am also being warned
that individual package files exceed the
hi, related to this, I found recently the problem that the
TxDb.Hsapiens.UCSC.hg38.knownGene package contains only a few of the
RN7SL (RNA component of signal recognition particle 7SL) genes and I
suspect the problem is that on the one hand UCSC currently provides the
'knownGene' track based
There are EnsDbs for Ensembl builds 87-111 that Johannes Rainier submits to the
AnnotationHub for those who want to use Ensembl mappings. And a direct build of
a TxDb using a UCSC GTF file has the chrM genes as well.
> ensdb <- hub[["AH100643"]]
> subsetByOverlaps(transcriptsBy(ensdb),
Due to a known issue
(https://github.com/lme4/lme4/issues/775#issuecomment-2024392388) running
lme4::lmer() fails in BioC 3.19 using R 4.4 2024-03-18 r86148 on the build site
because of a discrepancy between the Matrix version and the version used when
lme4 is compiled.
The solution is to
is this an argument in favor of using ENSEMBL gene and transcript IDs
rather than ENTREZ or UCSC? Or just changing the way that the databases
are keyed? There really ought not to be transcripts for a gene on a
different chromosome from the gene, although the MHC and KIR loci (with alt
contigs)
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,
As well as
> subsetByOverlaps(transcripts(Homo.sapiens), GRanges("chrM:1-16569"))
'select()' returned 1:1 mapping between keys and columns
GRanges object with 37 ranges and 2 metadata columns:
seqnames ranges strand | TXIDTXNAME
|
[1]
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
Dear Lori Sheperd - Kern
Awesome, thank you very much.
Have a great day :)
Oliver
De: "Kern, Lori"
À: "Olivier Cuvier" , "bioc-devel"
Envoyé: Jeudi 28 Mars 2024 12:19:38
Objet: Re: CuvierLab -Request to add maintainers for HicAggR
I can assist with this and will be in touch with
I can assist with this and will be in touch with Dr. Tesfaye to set up a
BiocCredentials account.
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
Dear Colleagues
I'd like to add Dr. Tesfaye - rob.t...@gmail.com - as a maintainer of CuvierLab
HicAggR GitHub-Bioconductor package.
Thank you for your help
Best regards
Oliver
Olivier Oliver Cuvier -
Group Leader (Director of Med Research (DR) / Inserm)
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