Dear Vilhelm,
notame seems to be an interesting package filling some gaps that currently
exist in the untargeted metabolomics workflow. I would strongly suggest to
support the SummarizedExperiment classes (in future). I would maybe suggest to
keep it as generic as possible without dedicated add
ke your Docker container. Then when you load
the object via data() R complains about missing the expected RCurl package.
That's just an educated guess, but seems plausible to me.
Best,
Mike
On Wed, 13 Mar 2024 at 10:10, Rainer Johannes
mailto:johannes.rai...@eurac.edu>> wrote:
Dear all
Dear all,
we're having some rather strange errors with R CMD check on the xcms package
recently: it will fail with this warning (which then becomes an error):
✔ checking whether the namespace can be loaded with stated dependencies (5.9s)
✔ checking whether the namespace can be unloaded cleanly
or
vignettes, this is why that particular package gets flagged only
there. Packages that forgot to add 'RUnit' to suggests, will get an
error on all platforms.
Adding 'BiocStyle' to Suggests: in the package DESCRIPTION file solves
this problem.
/Henrik
>
> Best,
>
Dear all,
I'm continuing to see some strange dependency problems for packages on the
linux build system for Bioconductor 3.17. First time I've seen them where on
the build report for snapshot 2023-03-31, and they are still there for snapshot
date 2023-04-02 (build report from 2023-04-03). What
Dear Bioc core,
after checking some build reports for a set of packages it seems that many are
failing due some recent updates with the macOS builder. The common theme seems
to be that for these packages (CRAN) dependencies "magick" and "rsvg" are not
available on macOS.
Just wanted to give a
ductor. All Bioconductor
> dependencies must be on CRAN or Bioconductor.
>
> Get Outlook for iOS
> From: Bioc-devel on behalf of Rainer
> Johannes
> Sent: Tuesday, March 2, 2021 4:36:05 AM
> To: bioc-devel
> Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for
Dear All!
in one of the xcms vignettes we are using a R package which is not yet in
Bioconductor and I added
Remotes:
RforMassSpectrometry/MsBackendMgf
to the DESCRIPTION thinking that on the BioC build machines the package might
get installed (from github). It does apparently not as we ge
ar issue on the support forum at
> https://support.bioconductor.org/p/p132470/
>
> The suggestion there was to try changing R's download.file.method option
> e.g. options(download.file.method = "curl")
>
> Best,
> Mike
>
> On Thu, 5 Nov 2020 at 13:21,
Dear all,
I'm unable to install the "msdata" package for the current BioC 3.13 release. I
keep getting the following error:
> BiocManager::install("msdata")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable)
(2020-10-24 r79367)
Installing package(s) 'msdata'
trying
27;s build report.
>
> Lori Shepherd
> 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 Rainer
> Johannes
> Sent:
dear all,
seems that the BioC package builder does not build the MsCoreUtils package even
after we bumped the version. The last change date listed in the BioC 3.12 check
results is "2020-06-23 06:08:43 -0400" and version 1.1.3 is listed, but in the
BioC git we have already version 1.1.5. Please
Hi Tom!
> On 28 Apr 2019, at 18:04, Thomas Lawson wrote:
>
> Hi BioConductor community,
>
> My package (msPurity) is passing the build on the Linux and Windows servers
> but has just started failing on the Mac OS X server due to the following
> error when running the "purityX" constructor in th
Dear all,
I like the new BiocManager package with its new possibilities to install
specific versions of Bioconductor - but what I miss is the possibility to
specify a local Bioconductor mirror from which to install packages.
Our calculation clusters don't have direct internet access, so I am mi
Hi Laurent,
I had the same problem with my ensembldb and FamAgg packages (guess the
duplicated commits were introduced by my old git-svn setup). The solution for
me was to iteratively do a git rebase (`git rebase -i ` with of the
last commit before any duplicates) removing all duplicated commi
conductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>>
>> From: Bioc-de
018-April/013156.html
>
> I think you should be able to get round it by including the name of Rd file
> you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I
> haven't actually tested this though).
>
> Mike
>
> On 16 April 2018 at 09:0
Dear all,
we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in
Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that
links to the method in MSnbase, that works nicely on Linux and mac
I recently had a similar problem with my FamAgg and ensembldb packages. I had
to remove the duplicated commits with `git rebase -i ` (i.e. interactive rebasing). During/after that I had to
fix some merge conflicts and ended overwriting my github master with the
cleaned history (`git push -f orig
from the git git-svn setup). I
could live with the git history not being clean. So, from my side, you could go
ahead and remove the pre-receive hook.
funnily, I have also duplicated commits in ensembldb, but there I'm still able
to push to Bioconductor git without problems.
best, jo
>
Dear all,
I'm unable to push my recent changes to FamAgg to the Bioconductor git repo
(see below for the error message). I did try the suggested fix but without any
success - seems the duplicated commits are in Bioconductor and not github.
thankful for any help or advise
The error message is:
l change to ensembldb (commit
> e4b9ffc54a35d8f4d8c398b94a53e0b65b48cbab) to fix a problem
> introduced by some recent changes to GenomicRanges so ensembldb
> should turn green again on Saturday's build report.
>
> Let me know if you still get problems.
>
> Cheers,
> H.
that is a cool feature -- I didn't even know it existed. it will be even
> cooler when it resumes working ;-)
>
>
>
> --t
>
> On Thu, Feb 8, 2018 at 2:34 PM, Rainer Johannes
> wrote:
> Dear all,
>
> one of the unit tests in ensembldb is failing beca
Dear all,
one of the unit tests in ensembldb is failing because of a problem in
GenomicFeatures::extractTranscriptSeqs (I guess):
library(BSgenome.Hsapiens.NCBI.GRCh38)
bsg <- BSgenome.Hsapiens.NCBI.GRCh38
library(EnsDb.Hsapiens.v86)
all <- extractTranscriptSeqs(bsg, EnsDb.Hsapiens.v86)
Error i
I'll test on mac and windows
cheers, jo
> On 7 Jan 2018, at 22:57, Neumann, Steffen wrote:
>
> Hi,
>
> Following the bug report in
> https://github.com/sneumann/mzR/issues/143
>
> there is a branch with a fix in
> https://github.com/sneumann/mzR/pull/144
>
> that passes Travis in
> https:
Thanks Herve
I did also fix it in ensembldb but didn't push to Bioc yet - well, have to pull
your changes now instead :)
cheers, jo
> On 20 Dec 2017, at 04:08, Hervé Pagès wrote:
>
> Hi Robert,
>
> Gviz depends on ensembldb which needed to have its NAMESPACE adjusted
> (i.e. import the path(
Dear all,
just wanted to inform you that I've implemented functions to map between
genomic coordinates and coordinates in transcripts and proteins (and vice
versa) in ensembldb (since all of the required data is available in EnsDb
packages).
I'm open to suggestions, improvements etc
cheers, j
Thanks Val
I'll fix that for `xcms`. Is it enough to fix the devel version, or should we
also fix the Bioc 3.6 release version?
cheers, jo
> On 29 Nov 2017, at 15:43, Obenchain, Valerie
> wrote:
>
> Hi developers,
>
> Several Bioconductor packages have been flagged as modifying 'library' du
Dear Martin,
> On 11 Oct 2017, at 13:05, Martin Morgan wrote:
>
> On 10/11/2017 03:48 AM, Rainer Johannes wrote:
>> Hi,
>> would it be possible to increase the allowed build and check times for mzR
>> on Windows? Building mzR takes very long due to the comp
Hi,
would it be possible to increase the allowed build and check times for mzR on
Windows? Building mzR takes very long due to the compilation of the included
proteowizard (and boost?) code so there is not much we can do to speed that up.
On linux and macOS all is fine, but we get TIMEOUT erro
all the args and
>> their defaults, tab-completion also works on the arguments, and the user
>> does not struggle in finding the man page (like s/he does sometimes
>> with generic and methods, especially when those are defined in
>> different packages).
>>
>> H.
Dear all!
We are currently implementing mzML write support in `MSnbase` and did
implement a `write` method for the S4 objects in `MSnbase`. Now, the
question is whether it might not be better to define a `write` S4
generic in `BiocGenerics`?
cheers, jo
Hi Aditya,
you could check the more recent ensembldb EnsDb databases to see if
there is something in them you might need/want.
I've added protein annotations to them (as provided by Ensembl). They
contain the Ensembl protein domains, the AA sequence, all protein domain
families (as defined/linked
Dear Riccardo,
I will look closer into this. In the meantime it might help if you try a
different binSize in the ObiwarpParam. Also, could you please add an issue with
this error on https://github.com/sneumann/xcms ? I can then track and relate
all changes to the issue.
thanks, jo
On 27 Jul 2
Dear all,
one of the xcms vignettes fails to build on tokay1 recently with the error
message:
Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe"
--quiet --pdf "xcmsDirect.tex" --max-iterations=20 -I
"C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I
"C:/Use
actually, I got quite some segfaults lately with the Ramp backend (was default
up to now). With the pwiz backend I don't get them anymore.
Also, in xcms we were manually setting the backend to pwiz and did not
experience any problems.
cheers, jo
On 23 May 2017, at 18:35, Laurent Gatto
mailto:l
to the package and after committing the change to
the Bioc svn ensembldb was synced successfully.
> aCGH actually had a RELEASE_3_5 branch; I'll investigate why aCGH and at
> least some other packages have not been fully updated after the branch.
>
> Martin
>
>
>>
>&
Hi,
the github mirror for ensembldb seems to be out of sync with the BioC svn, i.e.
the DESCRIPTION in
https://github.com/Bioconductor-mirror/ensembldb/blob/master/DESCRIPTION is
still at version 1.99.14 while in the svn it's already 2.1.0.
First I thought the sync is not yet finished, but the
An update: the fixed gap package is now in CRAN
(https://cran.r-project.org/web/packages/gap/index.html). Once the Windows
build machine uses/installs this updated CRAN package, the error in FamAgg will
be fixed.
cheers, jo
On 19 Apr 2017, at 13:04, Rainer Johannes
mailto:johannes.rai
titute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel
mailto:bioc-devel-boun...@r-project.org>> on
behalf of Rainer Johannes
mailto:johannes.rai...@eurac.edu>>
Sent: Wednesday, April 19, 2017
Dear all,
Somehow the FamAgg fails building with the recent R-3.4rc in Windows. I tracked
down the error and it comes from a fortran code in a function from the "gap"
CRAN package I'm using in one of the functions. I contacted the developer and
in the meantime implemented a workaround in FamAgg
to Bioc yet (asked Laurent for
that).
I did also fix wiggleplotr and made a pull request, but the developer did not
yet react to that.
cheers, jo
> https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html
>
> H.
>
>
> On 04/06/2017 01:07 PM, Rainer J
2017 at 10:05 PM, Michael Lawrence
mailto:lawrence.mich...@gene.com>
wrote:
Sorry I have been traveling. Will get to it soon.
On Apr 4, 2017 12:58 PM, "Rainer Johannes"
mailto:johannes.rai...@eurac.edu>>
wrote:
Hi Herve,
sorry for all the reds - actually I provided the patches to b
er path would have been to notify the maintainers
> of these packages first and wait that they make the required
> changes (i.e. to import the filters from AnnotationFilter)
> before modifying ensembldb. Maybe for next time ;-)
>
> Cheers,
> H.
>
> On 04/04/2017 04:02 AM, R
veloping without having to wait for Gviz?
These come from biovizBase which Gviz imports. I've sent Micheal the fixes for
biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for ensembldb I
get today still version 1.99.12 but not
Dear all,
I've just committed a change in ensembldb (version 1.99.13) that removes all
filter classes from it and imports them from the AnnotationFilter package. This
change will break biovizBase and ggbio (and all packages downstream of them,
e.g. Gviz). I've already sent Michael Lawrence patc
Do you have code fetching data from web resources? I also sometimes get timeout
errors on ensembldb and I guess it's because in some unit tests I'm fetching
data from the ensembl ftp server.
jo
> On 27 Mar 2017, at 18:37, Martin Morgan wrote:
>
> On 03/27/2017 12:22 PM, Aimin Yan wrote:
>> I
Dear all,
we are currently in the middle of refactoring and updating the xcms package,
which could cause (on the short term) some problems in packages depending on
functionality from xcms. In the long run everything should work and integration
of functionality from xcms in other packages should
Hi Steffen and Laurent,
one problem with xcms is that the 'devel' branch on sneumann/xcms is the real
'master' branch. I would suggest to create a new branch on github, e.g.
'biocdevel' and to link that one to the BioC svn (means also that
update_remotes.sh can not be user right away - the svn
Fixed in ensembldb
thanks Martin!
> On 14 Nov 2016, at 11:37, Martin Morgan wrote:
>
> An interested R-help thread (starting at
> https://stat.ethz.ch/pipermail/r-help/2016-November/443123.html) points out
> that return() is treated as a function by the R parser. This has some
> surprising
I just wanted to report that the github-mirror for ensembldb is out of sync
with the BioC svn.
You're most likely already working on that.
In any rate, thanks for your great work!
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/li
e how to best handle to problem. To sort your problem, we
>> (the MSnbase maintainers) could revert to our old initialize,Spectrum
>> method, but some very weird bugs (in R? in some very low-level C code?)
>> result in random crashes. We are looking for something else.
>
t run again into the random memory problems that we had in MSnbase
(issue https://github.com/lgatto/MSnbase/issues/138)
jo
> On 7 Oct 2016, at 20:14, Rainer Johannes wrote:
>
> we could try to switch back from the C-constructors to the "old" ones, I'll
> check
vel branch (which is in sync with BioC svn) as
I did have nasty merge conflicts doing a `git merge master`.
jo
> On 21 Sep 2016, at 13:38, Martin Morgan wrote:
>
> On 09/21/2016 12:01 AM, Rainer Johannes wrote:
>> Dear all,
>>
>> I recently observed that the svn and th
Dear all,
I recently observed that the svn and the github mirror of `ensembldb` is out of
sync. Is this something specific to `ensembldb` or is this a general problem?
Is there anything I could do to fix this?
thanks, jo
___
Bioc-devel@r-project.org
Dear all,
I wanted to update the EnsDb.* annotation packages I originally provided, but I
didn't find any guide how to do that in the "Developer resources" on the
Bioconductor website (although it could well be that I overlooked it).
How can I update my annotation packages?
thanks, jo
ote:
>
> On 05/02/2016 03:46 AM, Rainer Johannes wrote:
>> Hi Herve,
>>
>> passing down additional arguments to the internal exonsBy, cdsBy,
>> fiveUTRsByTranscript and threeUTRsByTranscript would do it! That
>> would be great, thanks.
>
> Hi Johannes --
box on EnsDb objects.
> Would that work?
>
> H.
>
> On 04/30/2016 04:05 AM, Rainer Johannes wrote:
>> Dear all,
>>
>> I was wondering, you think it would be possible to make the transcriptLength
>> function in GenomicFeatures a method and export that? Reason
Dear all,
I was wondering, you think it would be possible to make the transcriptLength
function in GenomicFeatures a method and export that? Reason is that I have
also implemented a transcriptLength function (actually presently a method in
order to allow that to be used for EnsDb and TxDb objec
Dear All!
Just wanted to let you know that I just pushed the last changes to the
ensembldb package (version 1.3.14) that allow an easier integration with
non-Ensembl based annotation. In detail, I’ve implemented the seqlevelsStyle
and seqlevelsStyle<- method from the GenomeInfoDb and now it’s p
> accepted by the "exonsBy" method for EnsDb objects.
>
> Let me know if you run into problems with this.
>
> Cheers,
> H.
>
> On 01/18/2016 06:46 AM, Rainer Johannes wrote:
>> Dear all,
>>
>> I’m having hard times to extend the extractTranscript
Dear all,
I’m having hard times to extend the extractTranscriptSeqs method implemented in
GenomicFeatures. Basically, I would like to implement a method for
signature(x="ANY”, transcripts="EnsDb”), so that I can re-use the method from
GenomicFeatures and add the optional parameter “filter” whic
Just as an info… EnsDb objects/packages (from ensembldb package) provide
similar functionality than the TxDb, are tailored to Ensembl annotations and
can be build from the GTF files from Ensembl (which can be fetched via
AnnotationHub; it’s all described in the ensembldb vignette).
cheers, jo
way in to annotation hub; this is against Sean's
>>> advice and I'm not really a big fan of this.
>>>
>>> I like the idea of being able to dynamically remap the seqlevels when the
>>> 2bit file is loaded by AnnotationHub, which would require Herve's
>>> sugge
an
>>> renaming the seqlevels. It also allows dropping, adding, and shuffling
>>> them. But you don't need to support all that. Supporting renaming would
>>> already go a long way. See selectMethod("seqlevels<-", "TxDb") in
>>> Genomic
the
>> hub, but I'm not sure how rtracklayer could automatically derive the
>> chromosome names.
>>
>> On Fri, Jan 8, 2016 at 2:37 AM, Rainer Johannes
>> wrote:
>>> dear all,
>>>
>>> I just run into a problem with a TwoBitFile I fetche
dear all,
I just run into a problem with a TwoBitFile I fetched from AnnotationHub. I was
fetching a TwoBitFile with the genomic DNA sequence, as provided by Ensembl:
> library(AnnotationHub)
> ah <- AnnotationHub()
> tbf <- ah[["AH50068”]]
> head(seqnames(seqinfo(tbf)))
[1] "1 dna:chromosome c
Dear all,
thanks to Vince’s suggestion I have now implemented the central AnnotationDbi
methods “columns”, “keys”, “keytypes” and “select” for EnsDb objects in my
ensembldb package version 1.3.11 (EnsDb are TxDb like annotation
packages/objects tailored to Ensembl based annotations). Thus, EnsD
OK, I have cleared the code duplications and pushed to my biovizBase and ggbio
forks.
Also, in the crunch method for EnsDb I’m avoiding now the loops. Thanks Michael!
jo
> On 15 Dec 2015, at 15:43, Rainer Johannes wrote:
>
> Thanks for the comments! I’ll make some changes and push a
o
> reduce this.
>
> Michael
>
> On Tue, Dec 15, 2015 at 1:37 AM, Rainer Johannes
> wrote:
>> OK, the modifications are in the repositories:
>> https://github.com/jotsetung/biovizBase
>> https://github.com/jotsetung/ggbio
>>
>> let me know if I can be of any
OK, the modifications are in the repositories:
https://github.com/jotsetung/biovizBase
https://github.com/jotsetung/ggbio
let me know if I can be of any help.
cheers, jo
On 14 Dec 2015, at 16:00, Rainer Johannes
mailto:johannes.rai...@eurac.edu>> wrote:
I’ll do, thanks for all comments
ges to your fork to make them easy for Michael and Tengfei to review.
Jim
On Mon, Dec 14, 2015 at 9:03 AM, Rainer Johannes
mailto:johannes.rai...@eurac.edu>> wrote:
dear Micheal,
github pull requests would also be my favorite way to contribute, but
unfortunately the Bioconductor-mirror
s like subset() and sort(). Like
> transcripts(sort(subset(db, seqname == "chr1"), by = geneSymbol)).
>
> Thanks,
> Michael
>
> On Mon, Dec 14, 2015 at 4:12 AM, Rainer Johannes
> wrote:
>> Dear all,
>>
>> I’ve modified the biovizBase and ggbio packa
Dear all,
I’ve modified the biovizBase and ggbio packages so that they do directly
support EnsDb annotations (just like annotations provided by TxDb
objects/packages).
Is there a way I could provide these changes? I’ve directly contacted Tengfei
last week, but did not get any reply yet…
cheers
Dear all,
I know that’s not a really urgent and important thing, but to me it seems that
the code coverage/test coverage badges are not calculated or updated anymore.
For example, on http://bioconductor.org/packages/devel/bioc/html/FamAgg.html it
says test coverage unknown suggesting that there
dear All,
we’re pleased to announce that our package, FamAgg, has been added to
Bioconductor. FamAgg provides methods to investigate familial aggregation in
large pedigrees and other pedigree analysis and plotting utilities.
cheers,
jo
___
Bioc-devel@
Could be that gcc via homebrew takes a while… especially if it is compiling
that stuff from source…
> On 18 Nov 2015, at 14:46, Ludwig Geistlinger
> wrote:
>
> While I am following Jo's suggestions on installing gcc via homebrew on my
> mac laptop (is it normal that the "make bootstrap" comma
Dear Ludwig,
I tried to install that package and it compiled nicely on my system with
> sessionInfo()
R Under development (unstable) (2015-10-20 r69547)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/
iff > Gviz.diff # ... as a diff for Florian
>
> ____
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
> Johannes [johannes.rai...@eurac.edu]
> Sent: Monday, November 09, 2015 10:08 AM
> To: bioc-devel@r-pro
wait until I receive all of you patches before adding them to
> the official package release.
> Florian
>
> On 09/11/15 16:08, "Bioc-devel on behalf of Rainer Johannes"
>
> wrote:
>
>> Dear All, dear Florian,
>>
>> I¹m currently working on a Gv
Dear All, dear Florian,
I’m currently working on a Gviz-hack that would enable to use the FaFiles
provided from AnnotationHub directly as SequenceTracks in Gviz. I think that
might be a nice addition, since that way both Ensembl based annotations (e.g.
as EnsDbs) and Ensembl genome fasta files
Dear Florian,
I’ve forked the (Bioconductor-mirror) Gviz repository on github and added
support to create GeneRegionTracks from EnsDb objects. It works analogously to
GeneRegionTracks from TxDb, but provides in addition gene or tx biotypes, gene
names and gene models of all (not only protein co
. I am working on it now and release
3.2 branches for all packages should be available soon.
Sorry for the confusion
Jim
On Oct 19, 2015 5:47 AM, "Rainer Johannes"
mailto:johannes.rai...@eurac.edu>> wrote:
Dear all,
somehow my ensembldb package is missing the release-3.2 branc
Dear all,
somehow my ensembldb package is missing the release-3.2 branch in the
Bioconductor-mirror repository on github. Is there something I should have done
myself? I thought that the branches are created automatically with each new
Bioconductor release.
Thanks for all suggestions and help
ne's exons and introns
geneSeqs <- getSeq(Dna, genes)
cheers, jo
On 09 Jun 2015, at 11:38, Rainer Johannes
mailto:johannes.rai...@eurac.edu>> wrote:
dear Ludwig,
On 09 Jun 2015, at 10:46, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johanne
update:
seems something is strange with the index... when I load the ensembl-77 DNA for
mouse I get two files, the fasta file and the index and I can extract the
sequences, while in the example below I just got the fasta file
On 10 Jun 2015, at 10:11, Rainer Johannes
mailto:johannes.rai
dear Ludwig,
On 10 Jun 2015, at 10:29, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johannes,
one follow-up question/comment on the EnsDb packages:
The reason they escaped my notice (and thus potentially will also others)
is that I expected such packages to be nam
rl_1.95-4.6
[23] RSQLite_1.0.0mime_0.3
[25] stringi_0.4-1BiocInstaller_1.18.2
[27] XML_3.98-1.2 httpuv_1.3.2
On 09 Jun 2015, at 16:25, Martin Morgan
mailto:mtmor...@fredhutch.org>> wrote:
On 06/08/2015 11:43 PM, Rainer Johannes wrote:
dear Robert
dear Ludwig,
On 09 Jun 2015, at 10:46, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johannes,
Thx for providing the great EnsDb packages!
One question:
As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes
dear Robert and Ludwig,
the EnsDb packages provide all the gene/transcript etc annotations for all
genes defined in the Ensembl database (for a given species and Ensembl
release). Except the column/attribute "entrezid" that is stored in the internal
database there is however no link to NCBI or
I wanted to ask whether it would be possible to export the functions
"fetchChromLengthsFromEnsembl" and "fetchChromLengthsFromEnsemblPlants" in
GenomicFeatures, as I find these methods quite useful to retrieve chromosome
lengths.
best, jo
___
Bioc-de
GRanges at some point.
cheers, jo
On 11 Apr 2015, at 00:54, Marc Carlson
mailto:mcarl...@fredhutch.org>> wrote:
On 04/10/2015 12:18 PM, Rainer Johannes wrote:
dear Sonali, Herve,
On 10 Apr 2015, at 19:59, Herv� Pag�s
mailto:hpa...@fredhutch.org><mailto:hpa...@fredhutch.org>>
wr
dear all,
I've build Ensembl based annotation packages (similar to the TxDb packages) for
Hsapiens, Mmusculus and Rnorvegicus for Ensembl versions 75 and 79 (Marc, I
have pushed them to the tracker, they should pass the R CMD check now).
If anybody wants some more species/Ensembl version just d
dear all!
I have submitted a new package that builds nicely on all machines except the
windows server "moscato2". I get a strange warning message, that I do not quire
understand: "Warning: multiple methods tables found for 'score'". I have no
function or method score defined in my package. Any
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