recipe r-biomartr

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', 'ENSEMBLGENOMES', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

Homepage

https://docs.ropensci.org/biomartr, https://github.com/ropensci/biomartr

License

GPL2 / GPL-2

Recipe

/r-biomartr/meta.yaml

package r-biomartr

(downloads) docker_r-biomartr

Versions

0.9.2-20.9.2-10.9.2-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install r-biomartr

and update with:

conda update r-biomartr

or use the docker container:

docker pull quay.io/biocontainers/r-biomartr:<tag>

(see r-biomartr/tags for valid values for <tag>)

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