date:20240328

Re: [Bioc-devel] Package size issue

2024-03-28 Thread Ali Sajid Imami

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 that that file is still part of the history. That should help
you cut down on the size.


Regards,
Dr. Ali Sajid Imami
LinkedIn 


On Thu, Mar 28, 2024 at 7:17 PM gabriel.villa...@mdc-berlin.de <
gabriel.villa...@mdc-berlin.de> wrote:

> 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 5MB size limit.
>
> The total size of a fresh clone of my package is 5.9MB, but 3.9MB of that
> is from the single packfile in .git/objects/pack. As I understand, the
> packfile contains the history of all files that have ever been in the
> repository, including files that have been deleted.
>
> I am wondering if this packfile is what is inflating my package size in
> the build and whether there is a solution to reduce its size. In case it is
> relevant: at some point a 1.38MB bam file was committed to the repo as toy
> data for running examples, but has since been deleted. I am also wondering
> why an individual file is reported to be exceeding 5MB when I don’t see any
> such file in my repo.
>
> Any advice would be very welcome!
>
> Best regards,
> Gabriel
> ___
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>

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[Bioc-devel] Package size issue

2024-03-28 Thread gabriel.villa...@mdc-berlin.de

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 5MB size limit.

The total size of a fresh clone of my package is 5.9MB, but 3.9MB of that is 
from the single packfile in .git/objects/pack. As I understand, the packfile 
contains the history of all files that have ever been in the repository, 
including files that have been deleted.

I am wondering if this packfile is what is inflating my package size in the 
build and whether there is a solution to reduce its size. In case it is 
relevant: at some point a 1.38MB bam file was committed to the repo as toy data 
for running examples, but has since been deleted. I am also wondering why an 
individual file is reported to be exceeding 5MB when I don’t see any such file 
in my repo.

Any advice would be very welcome!

Best regards,
Gabriel
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Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

2024-03-28 Thread Robert Castelo

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 on GENCODE annotations, but, on the other hand, 
they map them to Entrez IDs in a way in which they miss genes in that 
mapping. See the following example:

library(org.Hs.eg.db)
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

## fetch all the genes with 'RN7SL' in their official HGNC symbol
allsyms <- keys(org.Hs.eg.db, keytype="SYMBOL")
whrn7sl <- grep("RN7SL", allsyms)
length(whrn7sl)
[1] 687

## using org.Hs.eg.db build a map from Entrez IDs to Ensembl IDs
rn7slmap <- select(org.Hs.eg.db, keys=allsyms[whrn7sl], 
columns=c("ENTREZID", "ENSEMBL"),
    keytype="SYMBOL")
dim(rn7slmap)
[1] 687  3
head(rn7slmap)
    SYMBOL ENTREZID ENSEMBL
1  RN7SL1 6029 ENSG0276168
2 RN7SL4P 6030 ENSG0263740
3 RN7SL5P 6031    
4 RN7SL6P 6032    
5 RN7SL7P 6033    
6 RN7SL8P 6034    
all(!is.na(rn7slmap$ENTREZID))
[1] TRUE
sum(!is.na(rn7slmap$ENSEMBL))
[1] 666

as you see, org.Hs.eg.db provides Entrez IDs for all of the RN7SL genes 
and a map to most of the corresponding Ensembl gene IDs (666 out of 
687). However, when we look up how may of these genes are in 
TxDb.Hsapiens.UCSC.hg38.knownGene only 4 of them are present!

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
alltxdbEGs <- keys(txdb, keytype="GENEID")
sum(rn7slmap$ENTREZID %in% alltxdbEGs)
[1] 4

if you inspect the metadata of this TxDb package you'll see that it is 
based on GENCODE v44, let's build the TxDb object directly from the 
GENCODE v44 GTF file:

gencodetxdb <- 
makeTxDbFromGFF("https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz";)
allgencodeENSGs <- keys(gencodetxdb, keytype="GENEID")
head(allgencodeENSGs)
[1] "ENSG003.16" "ENSG005.6" "ENSG419.14"
[4] "ENSG457.14" "ENSG460.17" "ENSG938.13"

now let's try to see how many of the RN7SL genes in org.Hs.eg.db map to 
the original GENCODE annotations using the mapping in org.Hs.eg.db:

sum(rn7slmap$ENSEMBL %in% gsub("\\.[0-9]+$", "", allgencodeENSGs))
[1] 666

I guess the way in which UCSC maps Entrez IDs and Ensembl IDs could be 
improved, but obviously this is not our responsibility. What I wonder is 
whether we could build a more comprehensive TxDb package based on 
EntrezIDs. I'd say that ideally one would like to have a TxDb package 
with genomic annotations for every gene in org.Hs.eg.db, so that both 
org.Hs.eg.db and at least one of the TxDb.Hsapiens.* packages provided 
by Bioconductor have some minimum level of integrity.

robert.




On 28/3/24 16:31, James W. MacDonald wrote:
> 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), GRanges("MT:1-16569"))
> GRangesList object of length 37:
> $ENSG0198695
> GRanges object with 1 range and 11 metadata columns:
>seqnames  ranges strand |   tx_id tx_biotype
> | 
>[1]   MT 14149-14673  - | ENST0361681 protein_coding
>tx_cds_seq_start tx_cds_seq_end gene_id tx_support_level
>  
>[1]14149  14673 ENSG0198695 
>tx_id_version gc_content tx_external_name tx_is_canonical
> 
>[1] ENST0361681.242.6667   MT-ND6-201   1
>tx_name
>
>[1] ENST0361681
>---
>seqinfo: 457 sequences (1 circular) from GRCh38 genome
> 
>
>> z <- 
>> makeTxDbFromGFF(https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz)
> Import genomic features from the file as a GRanges object ... trying URL 
> 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz'
> Content type 'application/x-gzip' length 38959957 bytes (37.2 MB)
> ==
> downloaded 37.2 MB
>
> OK
> Prepare the 'metadata' data frame ... OK
> Make the TxDb object ... OK
> Warning message:
> In .get_cds_IDX(mcols0$type, mcols0$phase) :
>The "phase" metadata column contains non-NA values for features of type
>stop_codon. This information was ignored.
>> subsetByOverlaps(transcriptsBy(z), GRanges("chrM:1-16569"))
> GRangesList object of length 37:
> $ENST0386347.1
> GRanges object with 1 range and 2 metadata columns:
>seqnamesranges strand | tx_id   tx_name
>   |
>[1]

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

2024-03-28 Thread James W. MacDonald

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), GRanges("MT:1-16569"))
GRangesList object of length 37:
$ENSG0198695
GRanges object with 1 range and 11 metadata columns:
  seqnames  ranges strand |   tx_id tx_biotype
   | 
  [1]   MT 14149-14673  - | ENST0361681 protein_coding
  tx_cds_seq_start tx_cds_seq_end gene_id tx_support_level

  [1]14149  14673 ENSG0198695 
  tx_id_version gc_content tx_external_name tx_is_canonical

  [1] ENST0361681.242.6667   MT-ND6-201   1
  tx_name

  [1] ENST0361681
  ---
  seqinfo: 457 sequences (1 circular) from GRCh38 genome

> z <- 
> makeTxDbFromGFF(https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz)
Import genomic features from the file as a GRanges object ... trying URL 
'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.knownGene.gtf.gz'
Content type 'application/x-gzip' length 38959957 bytes (37.2 MB)
==
downloaded 37.2 MB

OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> subsetByOverlaps(transcriptsBy(z), GRanges("chrM:1-16569"))
GRangesList object of length 37:
$ENST0386347.1
GRanges object with 1 range and 2 metadata columns:
  seqnamesranges strand | tx_id   tx_name
 |
  [1] chrM 3230-3304  + |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 how the machine works rather 
than trying to change things that are set in stone. I mean I have tried many 
(many) times 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 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
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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) somewhat force 
the issue for that.  (we could discuss graph genomes here, but we aren't going 
to do that, because all gene->transcript->contig mappings start to break)

Omission of an entire chromosome seems... bad?  Regardless of the technical 
reason why.  There are arguments in favor of e.g. gene -> transcript -> contig 
where each relationship is potentially 1:many, but if chrM can't be sorted out 
then I am dubious that more complicated mappings can be efficiently handled.  
chrM is particularly weird in that it can have multiple haplotypes (i.e. 
contigs) even within the same cell, but at some point, simplifications are 
merited

--t

On Thu, Mar 28, 2024 at 10:12 AM James W. MacDonald 
mailto:jmac...@uw.edu>> wrote:
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] chrM 577-647  + |252799 ENST0387314.1
   [2] chrM648-1601  + |252800 ENST0389680.2
   [3] chrM   1602-1670  + |252801 ENST0387342.1
   [4] chrM   1671-3229  + |252802 ENST0387347.2
   [5] chrM   3230-3304  + |252803 ENST0386347.1
   ...  ... ...... .   ...   ...
  [33] chrM   5826-5891  - |252831 ENST0387409.1
  [34] chrM   7446-7514

[Bioc-devel] Issue with lme4/Matrix in BioC 3.19 R 4.4

2024-03-28 Thread Hoffman, Gabriel via Bioc-devel

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 update to Matrix 1.7 and then recompile lme4 from source.  
This will resolve the package failures in BioC 3.19

Best,
Gabriel




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

2024-03-28 Thread Tim Triche, Jr.

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) somewhat force the issue for that.  (we could discuss graph
genomes here, but we aren't going to do that, because all
gene->transcript->contig mappings start to break)

Omission of an entire chromosome seems... bad?  Regardless of the technical
reason why.  There are arguments in favor of e.g. gene -> transcript ->
contig where each relationship is potentially 1:many, but if chrM can't be
sorted out then I am dubious that more complicated mappings can be
efficiently handled.  chrM is particularly weird in that it can have
multiple haplotypes (i.e. contigs) even within the same cell, but at some
point, simplifications are merited


--t


On Thu, Mar 28, 2024 at 10:12 AM James W. MacDonald  wrote:

> 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] chrM 577-647  + |252799 ENST0387314.1
>[2] chrM648-1601  + |252800 ENST0389680.2
>[3] chrM   1602-1670  + |252801 ENST0387342.1
>[4] chrM   1671-3229  + |252802 ENST0387347.2
>[5] chrM   3230-3304  + |252803 ENST0386347.1
>...  ... ...... .   ...   ...
>   [33] chrM   5826-5891  - |252831 ENST0387409.1
>   [34] chrM   7446-7514  - |252832 ENST0387416.2
>   [35] chrM 14149-14673  - |252833 ENST0361681.2
>   [36] chrM 14674-14742  - |252834 ENST0387459.1
>   [37] chrM 15956-16023  - |252835 ENST0387461.2
>   ---
>   seqinfo: 711 sequences (1 circular) from hg38 genome
>
> However
>
> > subsetByOverlaps(transcriptsBy(Homo.sapiens), GRanges("chrM:1-16569"))
> GRangesList object of length 0:
> <0 elements>
>
> And
>
> > subsetByOverlaps(transcripts(Homo.sapiens, columns =
> c("GENEID","SYMBOL")), 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 |  GENEID  SYMBOL
> |  
>[1] chrM 577-647  + |
>[2] chrM648-1601  + |
>[3] chrM   1602-1670  + |
>[4] chrM   1671-3229  + |
>[5] chrM   3230-3304  + |
>...  ... ...... . ... ...
>   [33] chrM   5826-5891  - |
>   [34] chrM   7446-7514  - |
>   [35] chrM 14149-14673  - |
>   [36] chrM 14674-14742  - |
>   [37] chrM 15956-16023  - |
>   ---
>   seqinfo: 711 sequences (1 circular) from 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  On Behalf Of Vincent
> Carey
> Sent: Thursday, March 28, 2024 10:00 AM
> To: Tim 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", "SYMBOL")) 'select()' returned
> 1:1 mapping between keys and columns
>   ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
> 1 ENSG0198727 cytochrome b   CYTB4519
> > select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
> columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned
> 1:1 mapping between keys and columns
>SYMBOLGENENAME CDSCHROMGENEID
> 1 MTCYBP1 MT-CYB pseudogene 1  100499418
>
> relevant?
>
> On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. 
> 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.
> >
> > Be

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

2024-03-28 Thread 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=ENSG0198727;r=MT:14747-15887;t=ENST0361789


--t


On Thu, Mar 28, 2024 at 9:59 AM Vincent Carey 
wrote:

> 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   CYTB4519
> > select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
> columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL"))
> 'select()' returned 1:1 mapping between keys and columns
>SYMBOLGENENAME CDSCHROMGENEID
> 1 MTCYBP1 MT-CYB pseudogene 1  100499418
>
> relevant?
>
> On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. 
> 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@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
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Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

2024-03-28 Thread James W. MacDonald

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] chrM 577-647  + |252799 ENST0387314.1
   [2] chrM648-1601  + |252800 ENST0389680.2
   [3] chrM   1602-1670  + |252801 ENST0387342.1
   [4] chrM   1671-3229  + |252802 ENST0387347.2
   [5] chrM   3230-3304  + |252803 ENST0386347.1
   ...  ... ...... .   ...   ...
  [33] chrM   5826-5891  - |252831 ENST0387409.1
  [34] chrM   7446-7514  - |252832 ENST0387416.2
  [35] chrM 14149-14673  - |252833 ENST0361681.2
  [36] chrM 14674-14742  - |252834 ENST0387459.1
  [37] chrM 15956-16023  - |252835 ENST0387461.2
  ---
  seqinfo: 711 sequences (1 circular) from hg38 genome

However

> subsetByOverlaps(transcriptsBy(Homo.sapiens), GRanges("chrM:1-16569"))
GRangesList object of length 0:
<0 elements>

And

> subsetByOverlaps(transcripts(Homo.sapiens, columns = c("GENEID","SYMBOL")), 
> 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 |  GENEID  SYMBOL
|  
   [1] chrM 577-647  + |
   [2] chrM648-1601  + |
   [3] chrM   1602-1670  + |
   [4] chrM   1671-3229  + |
   [5] chrM   3230-3304  + |
   ...  ... ...... . ... ...
  [33] chrM   5826-5891  - |
  [34] chrM   7446-7514  - |
  [35] chrM 14149-14673  - |
  [36] chrM 14674-14742  - |
  [37] chrM 15956-16023  - |
  ---
  seqinfo: 711 sequences (1 circular) from 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  On Behalf Of Vincent Carey
Sent: Thursday, March 28, 2024 10:00 AM
To: Tim 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", "SYMBOL")) 'select()' returned 1:1 
mapping between keys and columns
  ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
1 ENSG0198727 cytochrome b   CYTB4519
> select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1 
mapping between keys and columns
   SYMBOLGENENAME CDSCHROMGENEID
1 MTCYBP1 MT-CYB pseudogene 1  100499418

relevant?

On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. 
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@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

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

2024-03-28 Thread Vincent Carey

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   CYTB4519
> select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
   SYMBOLGENENAME CDSCHROMGENEID
1 MTCYBP1 MT-CYB pseudogene 1  100499418

relevant?

On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. 
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@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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this email is intended only for the p...{{dropped:15}}

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

2024-03-28 Thread 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 
>  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]]
> 
> ___
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[Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

2024-03-28 Thread Kern, Lori via Bioc-devel

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]]

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Re: [Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

2024-03-28 Thread Olivier Cuvier

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 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 

From: Bioc-devel  on behalf of Olivier Cuvier 
 
Sent: Wednesday, March 27, 2024 6:29 PM 
To: bioc-devel@r-project.org  
Subject: [Bioc-devel] CuvierLab -Request to add maintainers for HicAggR 
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) 
Laboratory of Chromatin Dynamics - Functional Genomics 
Unit of Molecular Cellular and Dev. Biology (MCD) 
Center of Biology Integrative (CBI) / CNRS-Toulouse 
+33-659 75 42 70 
olivier.cuv...@inserm.fr 
olivier.cuv...@univ-tlse3.fr 
olivier.cuv...@gmail.com 
 


- Mail original - 
De: "Robel Tesfaye"  
À: "Olivier Cuvier"  
Envoyé: Mercredi 27 Mars 2024 19:10:08 
Objet: Re: HicAggR: demo on PlotAPA_byDistance and compare_to_background 
functions 

Salut Olivier, 

Peux-tu t'occuper de ça rapidement s'il te plaît? Le reviewing est en 
attente tant que je ne leur push pas la nouvelle version sur le git bioc 

On 26/03/2024 19:27, Robel Tesfaye wrote: 
> 
> Salut Olivier, 
> 
> Il n'y a que ton (olivier.cuv...@univ-tlse3.fr) compte qui peut mettre 
> à jour la version du package présent sur le git de bioconductor. 
> 
> Donc afin d'ajouter une liste de gens qui sont maintainers, tu dois 
> confirmer qu'on a droit de push des changements au git bioconductor. 
> 
> Si tu veux plus de détails sur mes échanges avec bioc 
> 
> [ 
> https://secure-web.cisco.com/1Zegt_Gn2IBgqTP0oVVXaW-DevkpyjF3ysopH2xJUwv37_qzuLYswgriq8Nc59u268Y5WTBWX97BGNreUt_-gGpevznmdMWLcBsjwYaI7Sif52zsGAsTaYv2fQFhwmgff13Cl17cl-oRT5O0f_VKLdrrWbHHQxMYoE9o1zic2BMwGaXsjo5DVUVgF4H7A8rVmuoiEKOFL1FQrM26fHeMOfTcstCW1Z5a1uRVCUhLXDmgGTudC5BmKfYANy6T6uFBEaOQKdf6BUxONpCwijkr09QtQBuWHDYAC_qX3EO__aMwEbWEgDbUAqSkWh7OFpPby/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2869
>  | 
https://secure-web.cisco.com/1Zegt_Gn2IBgqTP0oVVXaW-DevkpyjF3ysopH2xJUwv37_qzuLYswgriq8Nc59u268Y5WTBWX97BGNreUt_-gGpevznmdMWLcBsjwYaI7Sif52zsGAsTaYv2fQFhwmgff13Cl17cl-oRT5O0f_VKLdrrWbHHQxMYoE9o1zic2BMwGaXsjo5DVUVgF4H7A8rVmuoiEKOFL1FQrM26fHeMOfTcstCW1Z5a1uRVCUhLXDmgGTudC5BmKfYANy6T6uFBEaOQKdf6BUxONpCwijkr09QtQBuWHDYAC_qX3EO__aMwEbWEgDbUAqSkWh7OFpPby/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2869
 ] 
> 
> Comme tu n'as pas de compte personnel github (car CuvierLab est 
> désormais un compte organization), tu devrais soit créer un compte 
> github avec ce mail 
> 
> ou envoyer un mail à bioc-devel@r-project.org en mettant mon adresse
> mail (rob.t...@gmail.com) et ceux que tu veux ajouter en cc dans le mail.
> 
> Avec en en-tête par exemple: Request to add maintainers for HicAggR
> 
> merci, 
> 
> On 19/03/2024 10:50, Robel Tesfaye wrote: 
>> c'est cool merci. 
>> 
>> J'ai pensé aux variants justement pour dire que nos associations sont 
>> "bonnes". 
>> 
>> Il y a ce site [ 
>> https://secure-web.cisco.com/1G6fXBGvL5jOh1VtO00ca_nTjMDoDVfp5HtpJWYdNmFYE_HPqG4xrG_NWB_8piaaHxEUxL2oI9lQ8vveqwSscOE3LpGwqeaS-t_yW8YIsu7pzJLa8SQ68gZMSJnplL_yJdn0jZf3m78AbxpkOxHtb9NRG23dzaiC784Qy3ahO2egIuigfSyqza0blDVNSp2kfK_v6EHYuxEQp0UdlQHWsfSDDLBdqgNXrlhR4JFJ7NiCKpWb9ZKaCsbNh2T4q6YJHCZB-42uqC5CyPkBMcnWk31l7n1EO12XTXHSsa-KaATgElJJePw1Y-NwWuIhXNQuB/https%3A%2F%2Fwww.gtexportal.org%2Fhome%2Fgene%2FZBTB16
>>  | 
https://secure-web.cisco.com/1G6fXBGvL5jOh1VtO00ca_nTjMDoDVfp5HtpJWYdNmFYE_HPqG4xrG_NWB_8piaaHxEUxL2oI9lQ8vveqwSscOE3LpGwqeaS-t_yW8YIsu7pzJLa8SQ68gZMSJnplL_yJdn0jZf3m78AbxpkOxHtb9NRG23dzaiC784Qy3ahO2egIuigfSyqza0blDVNSp2kfK_v6EHYuxEQp0UdlQHWsfSDDLBdqgNXrlhR4JFJ7NiCKpWb9ZKaCsbNh2T4q6YJHCZB-42uqC5CyPkBMcnWk31l7n1EO12XTXHSsa-KaATgElJJePw1Y-NwWuIhXNQuB/https%3A%2F%2Fwww.gtexportal.org%2Fhome%2Fgene%2FZBTB16
 ] dans le 
>> quel sont répertoriés les eQTL de gènes d'intérêt. 
>> 
>> On aura peut-être pas les variants pour chacun de nos enhancers mais 
>> on peut confirmer certaines des associations je pense. 
>> 
>> On 19/03/2024 07:44, Olivier Cuvier wrote: 
>>> Un article à considérer peut-etre... 
>>> 
>>> 
>>> - Mail original - 
>>> De: "Olivier Cuvier"  
>>> À: "Robel Tesfaye"  
>>> Cc: "stephane schaak" , "Naomi SCHICKELE" 
>>>  
>>> Envoyé: Lundi 18 Mars 2024 19:11:16 
>>> Objet: Re: HicAggR: demo on PlotAPA_byDistance and 
>>> compare_to_background functions

Re: [Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

2024-03-28 Thread Kern, Lori via Bioc-devel

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


From: Bioc-devel  on behalf of Olivier Cuvier 

Sent: Wednesday, March 27, 2024 6:29 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

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)
Laboratory of Chromatin Dynamics - Functional Genomics
Unit of Molecular Cellular and Dev. Biology (MCD)
Center of Biology Integrative (CBI) / CNRS-Toulouse
+33-659 75 42 70
olivier.cuv...@inserm.fr
olivier.cuv...@univ-tlse3.fr
olivier.cuv...@gmail.com



- Mail original -
De: "Robel Tesfaye" 
�: "Olivier Cuvier" 
Envoy�: Mercredi 27 Mars 2024 19:10:08
Objet: Re: HicAggR: demo on PlotAPA_byDistance and compare_to_background 
functions

Salut Olivier,

Peux-tu t'occuper de �a rapidement s'il te pla�t? Le reviewing est en
attente tant que je ne leur push pas la nouvelle version sur le git bioc

On 26/03/2024 19:27, Robel Tesfaye wrote:
>
> Salut Olivier,
>
> Il n'y a que ton (olivier.cuv...@univ-tlse3.fr) compte qui peut mettre
> � jour la version du package pr�sent sur le git de bioconductor.
>
> Donc afin d'ajouter une liste de gens qui sont maintainers, tu dois
> confirmer qu'on a droit de push des changements au git bioconductor.
>
> Si tu veux plus de d�tails sur mes �changes avec bioc
>
> https://secure-web.cisco.com/1Zegt_Gn2IBgqTP0oVVXaW-DevkpyjF3ysopH2xJUwv37_qzuLYswgriq8Nc59u268Y5WTBWX97BGNreUt_-gGpevznmdMWLcBsjwYaI7Sif52zsGAsTaYv2fQFhwmgff13Cl17cl-oRT5O0f_VKLdrrWbHHQxMYoE9o1zic2BMwGaXsjo5DVUVgF4H7A8rVmuoiEKOFL1FQrM26fHeMOfTcstCW1Z5a1uRVCUhLXDmgGTudC5BmKfYANy6T6uFBEaOQKdf6BUxONpCwijkr09QtQBuWHDYAC_qX3EO__aMwEbWEgDbUAqSkWh7OFpPby/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2869
>
> Comme tu n'as pas de compte personnel github (car CuvierLab est
> d�sormais un compte organization), tu devrais soit cr�er un compte
> github avec ce mail
>
> ou envoyer un mail � bioc-devel@r-project.org en mettant mon adresse
> mail (rob.t...@gmail.com) et ceux que tu veux ajouter en cc dans le mail.
>
> Avec en en-t�te par exemple: Request to add maintainers for HicAggR
>
> merci,
>
> On 19/03/2024 10:50, Robel Tesfaye wrote:
>> c'est cool merci.
>>
>> J'ai pens� aux variants justement pour dire que nos associations sont
>> "bonnes".
>>
>> Il y a ce site 
>> https://secure-web.cisco.com/1G6fXBGvL5jOh1VtO00ca_nTjMDoDVfp5HtpJWYdNmFYE_HPqG4xrG_NWB_8piaaHxEUxL2oI9lQ8vveqwSscOE3LpGwqeaS-t_yW8YIsu7pzJLa8SQ68gZMSJnplL_yJdn0jZf3m78AbxpkOxHtb9NRG23dzaiC784Qy3ahO2egIuigfSyqza0blDVNSp2kfK_v6EHYuxEQp0UdlQHWsfSDDLBdqgNXrlhR4JFJ7NiCKpWb9ZKaCsbNh2T4q6YJHCZB-42uqC5CyPkBMcnWk31l7n1EO12XTXHSsa-KaATgElJJePw1Y-NwWuIhXNQuB/https%3A%2F%2Fwww.gtexportal.org%2Fhome%2Fgene%2FZBTB16
>>  dans le
>> quel sont r�pertori�s les eQTL de g�nes d'int�r�t.
>>
>> On aura peut-�tre pas les variants pour chacun de nos enhancers mais
>> on peut confirmer certaines des associations je pense.
>>
>> On 19/03/2024 07:44, Olivier Cuvier wrote:
>>> Un article � consid�rer peut-etre...
>>>
>>>
>>> - Mail original -
>>> De: "Olivier Cuvier" 
>>> �: "Robel Tesfaye" 
>>> Cc: "stephane schaak" , "Naomi SCHICKELE"
>>> 
>>> Envoy�: Lundi 18 Mars 2024 19:11:16
>>> Objet: Re: HicAggR: demo on PlotAPA_byDistance and
>>> compare_to_background functions
>>>
>>> Salut Robel, St�phane, Naomi
>>>
>>>
>>> Merci pour les Figures. Je regarde tout ca. Je ne sais pas sir j'ai
>>> d�j� dit que j'�tais en meeting � Lyon aujourd'hui et demain. Peu
>>> importe, c'est cool que tu aies pu regarder les figures de ton cot�.
>>> On peut en discuter mercredi apr�m si tu veux bien, ou vendredi.
>>> Disons que dans les perspectives du papier, il est important pour
>>> mon �quipe de garder la trame scientifique que nous avions fix�,
>>> avec un max de jolis r�sultats qui sont appuy�s par un bon
>>> positionnement de l'�quipe dans la th�matique. Bref, on en discutera.
>>>
>>> Bonne fin de journ�e � vous 3
>>> olivier
>>>
>>> - Mail original -
>>> De: "Robel Tesfaye" 
>>> �: "Olivier Cuvier" , "stephane
>>> schaak" , "Naomi SCHICKELE"
>>> 
>>> Envoy�: Lundi 18 Mars 2024 19:03:17
>>> Objet: HicAggR: demo on PlotAPA_byDistance and compare_to_background
>>> functions
>>>
>>> les figures que je vous parlais vendredi.
>>>
> --
> Robel Tesfaye
> Postdoc
> Team Chromatin Dynamics and Cell Proliferation
> UMR5077 CNRS-UPS, CBI
> 169 rue Marianne Grunberg-Manago
> 31400 Toulouse

--
Robel Tesfaye
Postd

[Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

2024-03-28 Thread Olivier Cuvier

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)
Laboratory of Chromatin Dynamics - Functional Genomics
Unit of Molecular Cellular and Dev. Biology (MCD)
Center of Biology Integrative (CBI) / CNRS-Toulouse
+33-659 75 42 70
olivier.cuv...@inserm.fr
olivier.cuv...@univ-tlse3.fr
olivier.cuv...@gmail.com



- Mail original -
De: "Robel Tesfaye" 
À: "Olivier Cuvier" 
Envoyé: Mercredi 27 Mars 2024 19:10:08
Objet: Re: HicAggR: demo on PlotAPA_byDistance and compare_to_background 
functions

Salut Olivier,

Peux-tu t'occuper de ça rapidement s'il te plaît? Le reviewing est en 
attente tant que je ne leur push pas la nouvelle version sur le git bioc

On 26/03/2024 19:27, Robel Tesfaye wrote:
>
> Salut Olivier,
>
> Il n'y a que ton (olivier.cuv...@univ-tlse3.fr) compte qui peut mettre 
> à jour la version du package présent sur le git de bioconductor.
>
> Donc afin d'ajouter une liste de gens qui sont maintainers, tu dois 
> confirmer qu'on a droit de push des changements au git bioconductor.
>
> Si tu veux plus de détails sur mes échanges avec bioc
>
> https://github.com/Bioconductor/Contributions/issues/2869
>
> Comme tu n'as pas de compte personnel github (car CuvierLab est 
> désormais un compte organization), tu devrais soit créer un compte 
> github avec ce mail
>
> ou envoyer un mail à bioc-devel@r-project.org en mettant mon adresse
> mail (rob.t...@gmail.com) et ceux que tu veux ajouter en cc dans le mail.
>
> Avec en en-tête par exemple: Request to add maintainers for HicAggR
>
> merci,
>
> On 19/03/2024 10:50, Robel Tesfaye wrote:
>> c'est cool merci.
>>
>> J'ai pensé aux variants justement pour dire que nos associations sont 
>> "bonnes".
>>
>> Il y a ce site https://www.gtexportal.org/home/gene/ZBTB16 dans le 
>> quel sont répertoriés les eQTL de gènes d'intérêt.
>>
>> On aura peut-être pas les variants pour chacun de nos enhancers mais 
>> on peut confirmer certaines des associations je pense.
>>
>> On 19/03/2024 07:44, Olivier Cuvier wrote:
>>> Un article à considérer peut-etre...
>>>
>>>
>>> - Mail original -
>>> De: "Olivier Cuvier" 
>>> À: "Robel Tesfaye" 
>>> Cc: "stephane schaak" , "Naomi SCHICKELE" 
>>> 
>>> Envoyé: Lundi 18 Mars 2024 19:11:16
>>> Objet: Re: HicAggR: demo on PlotAPA_byDistance and 
>>> compare_to_background functions
>>>
>>> Salut Robel, Stéphane, Naomi
>>>
>>>
>>> Merci pour les Figures. Je regarde tout ca. Je ne sais pas sir j'ai 
>>> déjà dit que j'étais en meeting à Lyon aujourd'hui et demain. Peu 
>>> importe, c'est cool que tu aies pu regarder les figures de ton coté. 
>>> On peut en discuter mercredi aprèm si tu veux bien, ou vendredi.
>>> Disons que dans les perspectives du papier, il est important pour 
>>> mon équipe de garder la trame scientifique que nous avions fixé, 
>>> avec un max de jolis résultats qui sont appuyés par un bon 
>>> positionnement de l'équipe dans la thématique. Bref, on en discutera.
>>>
>>> Bonne fin de journée à vous 3
>>> olivier
>>>
>>> - Mail original -
>>> De: "Robel Tesfaye" 
>>> À: "Olivier Cuvier" , "stephane 
>>> schaak" , "Naomi SCHICKELE" 
>>> 
>>> Envoyé: Lundi 18 Mars 2024 19:03:17
>>> Objet: HicAggR: demo on PlotAPA_byDistance and compare_to_background 
>>> functions
>>>
>>> les figures que je vous parlais vendredi.
>>>
> -- 
> Robel Tesfaye
> Postdoc
> Team Chromatin Dynamics and Cell Proliferation
> UMR5077 CNRS-UPS, CBI
> 169 rue Marianne Grunberg-Manago
> 31400 Toulouse

-- 
Robel Tesfaye
Postdoc
Team Chromatin Dynamics and Cell Proliferation
UMR5077 CNRS-UPS, CBI
169 rue Marianne Grunberg-Manago
31400 Toulouse

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[Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

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