Displaying 20 results from an estimated 40 matches for "biomart".
2010 May 31
3
after updating biomaRt cannot connect any more
I recently updated R 2.10.1 Patched (2010-02-20 r51163)
This morning I reinstalled biomaRt using biocLite.
Now I can no more connect to biomaRt and even the following instruction is hanging for a while until
the same error message pops up.
> listMarts()
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternati...
2009 Jun 16
1
Error using getBM() to query BioMart archives
I'm trying to identify the positions of all genes within a specific
chromosomal region using biomart. When using the current biomart
database I'm able to do this without issue. However, I need to use
build 36 of the mouse genome which was last included in ensembl mart
46. I selected this mart and the mouse dataset as follows:
mart<-useMart(biomart="ensembl_mart_46", host=&q...
2007 Jan 26
0
[BioC] problem with biomaRt getHomolog function
Steffen,
When the new biomaRt tries to load it errors out because I do not have
RMySQL installed. There is not a Windows binary for RMySQL and it does
contain C code that I do not know how to build.
I do not use the MySQL option in biomaRt. Does RMySQL need to be a
required dependency? Below is my screen output and sessionINfo...
2013 Feb 08
1
Conflict command getSequence {biomaRt} and getSequence {seqinr} !!
Hi !
Facing problem with " getSequence" commend .
when only biomaRt package loaded the following example working well
>mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
>seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart)
show(seq)
but when i have loaded the seqin...
2009 Nov 11
1
problems in installing biomart
Dear Forum
my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize
is that something is missing and it can't install XML, RCurl but I don't
know what more to do, I looked in previous posts but I did not find
infoprmation that helped.
Thanks
Andreia
biocLite("biomaRt")
Running biocinstall version 2.3.14 with R version 2.8.1
Your ve...
2009 Jun 23
1
Cannot install pakages from Bioconductor besides the default installation
I am running the last R version on SuSE 11.1.
I installed the Bioconductor environment following the instructions on the web. As a consequence some
core packages from Bioconductors were installed.
I need to add some more packages. So I tried biomaRt as follows.
It does not get installed correctly.
Please see the following sequence.
Thank you in advance.
Maura
> source("http://bioconductor.org/biocLite.R")
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In...
2009 Jun 23
2
question about package biomaRt
Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..?
Thank you very much.
Maura
tutti i telefonini TIM!
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2018 Mar 21
0
Error in GDCprepare step of TCGAbiolinks
...o error. Thus i have uninstalled and
again installed the R but the error is not going.
Today i have installed the developer version of TCGAbiolinks. and the error
is still there.
I have attached the code used and the session info.
Every time i run this GDCprepare command this same error comes as biomart
service is not available. So i had contaced the Biomart people but they
said that the Biomart is working fine.
below is the complete R code i am usign with the corresponding error,
library(TCGAbiolinks)
query.exp <- GDCquery(project = "TCGA-LUAD",
data.category...
2011 Feb 15
1
getBM in biomaRt
I'm using 'getBM' function in Bioconductor package 'biomaRt' to retrieve gene ids based on known chromosome locations.
The question is getBM just only return one gene id once a time, even a query is mapped to multiple genes. What's the criteria for picking that special one?
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2013 May 07
1
Problem with biomaRt::getSequence.
... No UTR is annotated for this transcript 10644
Problem 2:Problem is here
protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide", mart=ensembl)
Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, :
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2)
I need help please.
/.......Tanvir Ahamed
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2020 Jun 09
5
R 4.0.0 rebuild status
Over the last several days, I've been working hard to get all of the Fedora
R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With
the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and
R-rtracklayer, I believe everything is built and updated to the latest
versions. And of those packages, they're all ready to go when Fedora
infrastructure is working reliably again (the great datacenter migration
has started and I can no longer git push). I...
2020 Jul 06
2
R 4.0.0 rebuild status
...fc.up.pt> wrote:
> On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote:
> > Over the last several days, I've been working hard to get all of the
> Fedora
> > R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag).
> With
> > the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and
> > R-rtracklayer, I believe everything is built and updated to the latest
> > versions. And of those packages, they're all ready to go when Fedora
> > infrastructure is working reliably again (the great datacenter migration
> > has...
2010 May 28
1
why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
I executed the following lines several times from a script as well as pasting them in an R shell.
Systematically biomaRt is failing.
The problem is to extract the 3UTR sequences corresponding to a vector containing 1941
Ensembl Transcript numbers (some are duplicated ... is this s problem ?)
Please, find the failing instructions in the following including the ENST vector
Any suggestion is welcome. Thank you,
Maura...
2007 Feb 05
3
RSNPper SNPinfo and making it handle a vector
If I run an analysis which generates statistical tests on many SNPs I would
naturally want to get more details on the most significant SNPs. Directly
from within R one can get the information by loading RSNPer (from
Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately,
the command cannot handle a vector and therefore only wants to do one at a
time.
I tried the lapply and
2010 Jul 08
2
package installation for Windows 7
...defining ?biocinstallRepos?
> biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] "affy" "affydata" "affyPLM" "affyQCReport"
[5] "annaffy" "annotate" "Biobase" "biomaRt"
[9] "Biostrings" "DynDoc" "gcrma" "genefilter"
[13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma"
[17] "marray" "multtest" "vsn" "xtable"
Please wait...
Warning in in...
2018 Sep 18
2
Suggested Patch: Adding commas to list of packages after R CMD check
...parseNet' version '0.99.13'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Packages required but not available:
'MultiAssayExperiment' 'glmnet' 'SummarizedExperiment' 'STRINGdb'
'biomaRt' 'futile.logger' 'sparsebn' 'sparsebnUtils' 'forcats'
'dplyr' 'readr' 'ggplot2' 'ggfortify' 'reshape2' 'rlang' 'loose.rock'
Packages suggested but not available:
'testthat' 'knitr' '...
2008 Sep 17
2
RCurl compilation error on ubuntu hardy
...st members,
I encountered this problem and the solution pointed out in a previous
thread did not work for me.
(e.g. install.packages("RCurl", repos = "http://www.omegahat.org/R")
I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get.
I really need RCurl in order to use biomaRt ... any help would be
greatly appreciated.
Best wishes,
Emmanuel
=================================================
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC...
2010 Sep 04
1
non-zero exit status error when install GenomeGraphs
...DLLpath = DLLpath, ...) :
unable to load shared library
'/apps/rhel5/x86_64/R/R-2.10.1//lib64/R/library/
XML/libs/XML.so':
libxmlsec1.so.1: cannot open shared object file: No such file or directory
Error : .onLoad failed in 'loadNamespace' for 'XML'
Error : package 'biomaRt' could not be loaded
ERROR: lazy loading failed for package 'GenomeGraphs'
* removing
'/userhom2/3/cchen1/R/x86_64-unknown-linux-gnu-library/2.10/GenomeGra
phs'
The downloaded packages are in
'/tmp/Rtmp3wsJxw/downloaded_packages'
Warning message:
In install.pack...
2020 Jun 09
0
R 4.0.0 rebuild status
On Tue, 9 Jun 2020 at 04:42, Tom Callaway <tcallawa at redhat.com> wrote:
>
> Over the last several days, I've been working hard to get all of the Fedora
> R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With
> the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and
> R-rtracklayer, I believe everything is built and updated to the latest
> versions. And of those packages, they're all ready to go when Fedora
> infrastructure is working reliably again (the great datacenter migration
> has started and I can no...
2020 Jul 06
0
R 4.0.0 rebuild status
On Tuesday, 9 June 2020 03.40.52 WEST Tom Callaway wrote:
> Over the last several days, I've been working hard to get all of the Fedora
> R packages rebuilt against R 4.0 in rawhide (in the F33-R-4 side tag). With
> the exception of R-biomaRt, R-BSgenome, R-GenomicAlignments, and
> R-rtracklayer, I believe everything is built and updated to the latest
> versions. And of those packages, they're all ready to go when Fedora
> infrastructure is working reliably again (the great datacenter migration
> has started and I can no...