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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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Alternative Biomart Hosts

I am trying to run the following Biomart script (params$species == "rabbit"){ ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="ocuniculus_gene_ensembl", host="uswest.ensembl.org", …
Rob Staruch
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Error in EnsDb.Hsapiens.v86 package to convert ensembl to symbol

I installed package EnsDb.Hsapiens.v86 to convert genes ensembl to symbol, after trying many packages that's the best one to conversion with less NAs. I tried to write the code but I got unsual error, here's my…
Hicham Hboub
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Is it possible to annotate ALL myIDs from Ensembl to symbol using R (biomaRt)?

I have a human datasets with genes ensembl and I want to annotate IDs to Symbol instead of ensembl in one of these datasets I have exactly 20176 genes I used two methods, but in boths I got NAs in some genes First…
Hicham Hboub
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How to install biomaRt from bioconductor

I need biomaRT but it is not installing. How do I fix this? BiocManager::install("biomaRt") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN:…
ksci
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CURL_OPENSSL_3 problem while installing biomaRt R package on Ubuntu 20.04

Problem I am trying to install biomaRt R package, but I have been experiencing problems. I have also noticed that the same problem also occurs with some other packages like twitteR. It seems like it is a problem related to curl. When I run the…
Ali Altıntaş
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loop function i r code for large data file

I am having same issue Query genes within regions but data is huge and creating certain issue. My data is like 1 10000 11000 1 20000 21000 . . . . . . . . . 1 1000000 1001000 . . …
Arora
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bioconductor and R, error in the use of getBM() function when trying to retrieving the sequence of genes

I'm trying to use the getBM() function of bioconductor to retrieve the sequences of some gene. Here's my script: setwd(".") options(stringsAsFactors = FALSE) cat("\014") if (!requireNamespace("BiocManager", quietly = TRUE)) …
DavideChicco.it
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Excel: Ensembl continue, how to save to CSV file after change R

Related to Unable to use biomaRt package to get Gene Symbols from Entrez IDs The code is working like a charm, but I would like to save it to my current CSV file and not only "viewing" it (adding an additional column will do the work as well, I got…
TheUndecided
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Arabidopsis Gene ID Conversion (BioMart, CLC Genomics Workbench Output)

I have an output of RNA-seq reads from CLC genomics workbench, for Arabidopsis thaliana. The list of genes contains a mix of gene names (i.e. "TRY", "TMM", "SVP", "FLC"), and IDs (e.g. "AT1G01390", "AT1G01310", "AT1G01240"). I would like to convert…
James Fischer
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R - Using biomaRt/getBM generates a list of 55,000+ genes instead of the ~15,000 I'm inputting as a data frame under "values"

I have downloaded an extensive dataset from NIH GEO and am attempting to convert the Ensembl names in the first column to MGI symbols The table I've named SOD is shown below SOD Data - Total rows = 15,396 I used the following…
mikephel
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Can i use biomart to map gene names, omim numbers and chromosome locations?

I have extracted from some texts informations about genes and chromosomes in object to classify a database of some texts. my result missed some informations; in fact some texts could contain just the gene name and the location and i want to get the…
aida abidi
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How to change two variables using lapply and biomart

I have used lapply along with biomart to extract the homologues for 3 different species. I also need to extract the target IDs for all of the homologues and I was hoping to also use lapply for the target IDs as well to make my code more efficient.…
Jack Dean
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Another issue with lapply and BioMart

I recently asked a question about lapply, but now I've changed my approach and ran into more problems I can't resolve. This is the code I'm having issues with: Load biomaRt library(biomaRt) Make the hsapiens mart ensembl_hsapiens <-…
Jack Dean
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biomaRt: Cannot access the zebra fish dataset

I cannot access the zebra fish ensembl database with biomaRt in R... # biomaRt library (biomaRt) listMarts() ensembl <- useMart("ensembl") listDatasets(ensembl) #output is really bad, with huge spaces between lines (cannot copy it…
francoiskroll
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How to use NCBI gene database in biomaRt R package

I'm not very expert with R but I'm trying to learn ho to use the biomaRt package to find genes located in my regions of interest. I've managed to produce a valid output using the ensembl dataset with the following code: > mart=…
Francesca Scellato
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