biomaRt

biomaRt – R Interface to BioMart and Ensembl

biomaRt is an R/Bioconductor package that provides programmatic access to BioMart services. It is widely used to query EMBL-EBI’s Ensembl database from within R, enabling users to retrieve gene, transcript, protein, sequence, annotation, and identifier information in reproducible analysis workflows. biomaRt supports flexible database queries and helps integrate biological annotations directly into downstream bioinformatics analyses.

Key benefits
Provides an R interface to BioMart services
Enables programmatic access to Ensembl annotations
Supports reproducible retrieval of gene, transcript, and protein information
Facilitates identifier mapping and annotation enrichment
Integrates smoothly into R and Bioconductor workflows
Applications
Querying Ensembl from R
Gene, transcript, and protein annotation retrieval
Identifier conversion and mapping between database accessions
Extraction of genomic coordinates and sequence-related metadata
Integration of annotation data into omics analysis pipelines
Intended use

biomaRt is intended for bioinformaticians, genomics researchers, transcriptomics researchers, Bioconductor users, and life scientists who need programmatic access to biological database annotations. It is particularly suited for workflows that require reproducible annotation retrieval, identifier mapping, or integration of Ensembl data into R-based analyses.

Contact:
Website https://github.com/Huber-group-EMBL/biomaRt/issues