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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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R how to install a specified version of a bioconductor package?

The current version of the package I would like to use is failing on bioconductor. Yet, the old version used to work. I am wondering how one can install a specific version of a bioconductor package? Thanks in advance. In my case, the package is…
anilbey
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Error with R package biomaRt and This dependency RSQLite

I have a problem to install biomaRt with bioconductor. I have already install this package without error in Rstudio with R 3.6 but with R 4.0 in conda specific environment container, I have an error with RSQLite. Here this message…
William Jarassier
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Convert GENCODE IDs to Ensembl - Ranged SummarizedExperiment

I have an expression set matrix with the rownames being what I think is a GENCODE ID in the format for example "ENSG00000000003.14" "ENSG00000000457.13" "ENSG00000000005.5" and so on. I would like to convert these to gene_symbol but I am not sure…
r_mvl
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Best way to get list of SNPs by gene id?

I have a long data frame of genes and various forms of ids for them (e.g. OMIM, Ensembl, Genatlas). I want to get the list of all SNPs that are associated with each gene. (This is the reverse of this question.) So far, the best solution I have found…
CoderGuy123
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Looping with biomart in R

I have a dataset list that I created based on many files. list.function <- function() { sample1 <- data.frame(ensembl.id = c("ENSG00000000005.6", "ENSG00000000003.15", "ENSG00000000419.13", "ENSG00000000457.14", "ENSG00000000460.17"),…
Gabriel G.
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R biomaRt package: obtaining all values in linked databases

A bioinformatics programming question. In R, I have a classic speciesA-to-speciesB gene symbol conversion, in this example from mouse to human, which I'm performing using biomaRt, and specifically the getLDS…
Federico Giorgi
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Internal Server Errors when querying biomart?

When executing R commands with the biomaRt package, I often get the error "Internal Server Error (HTTP 500)." with basic commands like ensembl<-useMart("ensembl") ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") These commands…
AldehydeDeva
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convert Ensembl ID to gene name using biomaRt

I have a dataset called kidney_ensembl and I need to convert Ensembl IDs to gene names. I'm trying the code below, but it's not working. Can somebody help me? I know there are similar questions, but they are not helping me. Many thanks! converting…
Fabiano Pinheiro Da Silva
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Entrez gene IDs from gene list using biomaRt

I am trying to convert a list of gene names to entrez gene IDs. for now i have this: >library(biomaRt) >ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") >mapping <- getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id', …
Laurent Winckers
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Pearson's correlation coefficient with from two tables in r

I have the two data sets below: df <- read.table(text = "Human_Gene_Name hsapiens mmusculus ggallus celegans dmelanogaster cintestinalis trubripes xtropicalis mmulatta A1CF 5.634789603 4.787491743 3.688879454…
Jack Dean
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Query genes within regions

I want to retrieve the genes that are present within a series of regions. Say, I have a bed file with query positions such like: 1 2665697 4665777 MIR201 1 10391435 12391516 MIR500 1 15106831 17106911 MIR122 1 …
Emilio Mármol Sánchez
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Why is Biomart giving different number of paralogues to the ensembl website?

This is the code I am using to extract paralogues for the AA792892 gene: source("https://bioconductor.org/biocLite.R") biocLite("biomaRt") library(biomaRt) ensembl_mouse <- useMart("ensembl", dataset =…
Jack Dean
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Counting the number of paralogues for mouse genes gives me the wrong frequency

I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. We think it is because some genes have one to…
Jack Dean
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Error message when using Biomart hsapiens_gene_ensembl dataset. Anyone know how to solve?

Here is my code that I used to try to connect to the hsapiens dataset: > mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", + dataset = "hsapiens_gene_ensembl", + host =…
ScottSchumacker
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retrieve SNP location in biomaRt, command hangs

I was trying to retrieve information on a SNP location. I tried to follow the instructions of an answer from this website, but the command doesn't work anymore: library(biomaRt) # biomaRt_2.30.0 snp_mart = useMart("ENSEMBL_MART_SNP",…
RDlady
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