similar to: [BioC] problem with biomaRt getHomolog function

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

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 seqinr, i got problem

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",

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

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 version of R requires version

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. Alternatively the

Dear Sir/ma'am, I'm using R-3.4.4 and TCGAbiolinks package for the analysis of GDC data. Till today i have reintalled R and R studio for 5 times but one error comes when i analyze the GDC data at the step GDCprepare. the data i am using is not a legacy data of GDC data portal. I think the problem is with my Laptop only because i have run the same commands in another PC and there was no

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! [[alternative HTML version deleted]]

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? [[alternative HTML version deleted]]

Dear R colleagues, I annotated a list of single nuclotide polymorphiosms (SNP) with the corresponding genes using biomaRt. The result is the following data.frame (pasted from R): snp ensembl_gene_id 1 rs8032583 2 rs1071600 ENSG00000101605 3 rs13406898 ENSG00000167165 4 rs7030479

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

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 >

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

R-BiocFileCache is now branched for f32 (finally). You should be able to build it if/when the PDC comes back up. Lotta random outages right now. Tom On Mon, Jul 6, 2020 at 10:40 AM Jos? Ab?lio Matos <jamatos at 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 >

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

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

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

On 18/09/2018 2:16 PM, Marcel Ramos wrote: > Dear R-devs, > > > Scenario: > > When checking a package via `R CMD check package_tar.ball`, required / suggested packages may be missing. R subsequently returns a list of packages that are missing (delimited by spaces). > > Example: > > ``` > R CMD check glmSparseNet_0.99.13.tar.gz > * using log directory

Dear R users, There is a error message when I run the following code. It is used to load microarray data and use the top 1000 genes for training svm to classify test set . > library(e1071) Loading required package: class > f=read.table("F:\\lab\\ microarray analysis\\VEH LPS\\exprs.txt",

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =