biomaRt

"biomaRt" is a tool that facilitates the integrated bioinformatic analysis of genomic experiments by providing a computational environment in R. The tool utilizes BioMart web services to establish relationships and mappings between DNA sequences, copy number variation, mRNA, and protein abundance data. It allows users to programmatically access and integrate data from public databases such as Ensembl, offering flexibility and reproducibility in bioinformatic analyses. The tool addresses challenges related to gene-to-transcript-to-protein mappings, providing a comprehensive solution for researchers working with diverse biological datasets.

Topic

Data acquisition;Database management;Model organisms;Molecular interactions, pathways and networks;Zoology

Detail

  • Operation: Database search;Data retrieval;Structural similarity search;Query and retrieval

  • Software interface: Command-line user interface

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 2.58.0

  • Credit: U24 CA126551 grant.

  • Input: -

  • Output: -

  • Contact: Mike Smith grimbough@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
  • Durinck S, et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. 2009; 4:1184-91. doi: 10.1038/nprot.2009.97
  • https://doi.org/10.1038/nprot.2009.97
  • PMID: 19617889
  • PMC: PMC3159387

Download and documentation

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