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Questions tagged [biomart]

biomaRt is a Bioconductor package. Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

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Get gene location from gene symbol and ID

I want to get gene location of human genome from gene symbol(example: TTN) and gene ID(example: ENSG00000155657). I want to do it using biomaRt package of R. How can I do that?
asdlfkjlkj
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Unable to use biomaRt package to get Gene Symbols from Entrez IDs

I am using the following code to retrieve Gene Symbols from Entrez IDs: library("biomaRt") ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org") g <- getBM(c("hgnc_symbol"), filters = "entrezgene",…
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Error when Using BiomartGeneRegionTrack in cummeRbund package

I am trying to plot a gene of interest using cummeRbund package. Using this script: biomTrack<-BiomartGeneRegionTrack(genome=genome, chromosome=as.character(myChr), start=myStart, end=myEnd, name="ENSEMBL", showId=T) I encountered this error: …
user3275043
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Annotate positions using biomaRt

I have some genome positions and I want to annotate these positions (find Ensembl gene ID, the features like exonic, intronic, ...) based on Ensembl using biomaRt R package. part of my data chr start stop strand chr10 100572320…
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How do I use biomaRT to get the corresponding gene iDs

I have a txt file and it looks like this. I need to use biomaRT in R to get the corresponding gene IDs of a whole list of different Refseq and peptides. Along with that, I need to keep the peptide sequence with the final outcome How would I do that?…
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Why do I have a different amount of estimated gene counts?

I am analyzing bulk RNA seq data and I used Kallisto to align my data to the transcriptome. Then, I used tximport to assign the gene names from ensembl to my counts. I am comparing the results I analyzed currently to some data that were run 4 years…
pythonbeginner
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Can't convert dog ensembl IDs into gene names

I usually use biomaRt to convert gene ids to symbols. However, this time the ensembl IDs I have (for a dog) do not match the ensembl ids of biomart dataset "clfamiliaris_gene_ensembl". I also tried to use the ensembl web portal, the dog dataset is…
Yulia Kentieva
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biomaRt getBM not working due to getNodeSet {XML} error

I'm running the following code in r and it is not working. getBM seems to not work for any arguments. Am I doing something wrong? ibrary(biomaRt) ensembl <- useEnsembl(biomart = "genes") ensembl <- useEnsembl(biomart = "ensembl", …
wkde
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Converting mouse Ensembl ID's to gene names in a data frame

I have recently produced an unsupervised hierarchical cluster heat map using 30 different RNA-seq samples. The x axis is labelled as the name of each sample, and the y axis displays the 100 most variable genes presented as mouse Ensembl ID's (e.g.…
Lauren McKenzie
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Trying to convert Ensembl ID to gene name in R (biomaRt)

I have a large dataset of gene expression data and I'm trying to convert the gene identifiers into gene names using biomaRt in RStudio, but for some reason when I use the merge function on my data frames, my entire data table is merged wrong/erased.…
Just A Mathematician
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Converting ENSEMBL IDs to Gene ID in a Data Frame

I have a large data-table of RNA-seq data that is listed by ensembl_gene_id, but I would like to convert to hgnc_symbol, for ease of visualization on heat maps. So far I have the following code - but not sure how to proceed. Would it be better to…
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Get hgnc_symbol/gene_name from ensembl_gene_id

I have this code (come from here): library('biomaRt') mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) genes <- rownames(res) G_list <- getBM(filters= "ensembl_gene_id", attributes=c("ensembl_gene_id","entrezgene",…
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Install biomaRt package (R version 3.5.2) for linux (Ubuntu for Windows)

I am trying to install Biomart package, and I used this code: source("https://bioconductor.org/biocLite.R") biocLite("biomaRt") library("biomaRt") and I get this warning message: Warning messages: 1: In install.packages(pkgs = doing, lib…
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converting from Ensembl gene ID's to different identifier

I've inherited a dataset of RNAseq output data from Canis Lupus (dog). I have the gene identifier in the Ensembl format, specifically they look like this, ENSCAFT00000001452.3. I am trying to use bioMaRt to convert them to a more common ID and need…
Ryan T.
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How to extract prosite patterns for Ciona intestinalis using Biomart

By using Biomart I have been able to extract prosite patterns for a list of genes for a few species. e.g. for humans, to extract the prosite patterns start for the foxa3 gene, I would use the code: library(biomaRt) ensembl[["hsapiens"]] <-…
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