biomartr

Provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The biomartr package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, biomartr communicates with the BioMart database for functional annotation of retrieved sequences.

biomartr specifications

Desktop

Information

Unique identifier	OMICS_15284
Name	biomartr
Software type	Package/Module
Interface	Command line interface
Restrictions to use	Academic or non-commercial use
Operating system	Unix/Linux, Mac OS, Windows
Programming languages	R
License	GNU General Public License version 3.0
Computer skills	Advanced
Version	0.9.9000
First release date	2016
Stability	Stable
Requirements	biomartr, rtools, abide
Source code URL	https://cran.r-project.org/web/packages/biomartr/index.html
Maintained	Yes

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Versioning

No version available

Documentation

Documentation: https://cran.r-project.org/web/packages/biomartr/biomartr.pdf
Issues: https://github.com/HajkD/biomartr/issues

Maintainer

Hajk-Georg Drost

Publication for biomartr

Biomartr: genomic data retrieval with R

2017 Bioinformatics

PMCID: 5408848

PMID: 28110292

DOI: 10.1093/bioinformatics/btw821

biomartr institution(s)

The Sainsbury Laboratory, University of Cambridge, Cambridge, UK

biomartr funding source(s)

This work was supported by an European Research Council grant named EVOBREED [grant number 322621] and a Gatsby Fellowship [grant number AT3273/GLE].

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