Questions tagged [biomart]

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Retrieving all genes for a gene ontology term

I'm looking for an easy way to retrieve all the genes in a list that are associated with a certain GO term, preferably using R/Bioconductor packages. I'm not interested in under/overrepresentation or ...
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How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
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Error in checkDataset, The given dataset: mmusculus_gene_ensembl , is not valid

I was perfectly using bioMart, but it gave an error, I went ahead trying to follow the following thread. And there were some issues with ...
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Cannot connect to BioMart webservice in R script, how to troubleshoot connection?

I'm attempting to query from BioMart in R using the biomaRt package with a script I've used many times before. I connect to the service with this line of code: ...
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1answer
108 views

Too slow issue of BioMart

I am using library(biomaRt) in R to annotate SNP rsid. It takes too much time for only 1000 SNPs....... I would like to know how I can run this code faster. ...
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40 views

Getting all promoters of a specific gene

I'd like to perform a motif analysis of all promoter regions of the gene ENSMUSG00000020538 in mus musculus. To do so, I wanted to use Biomart : ...