Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) ) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) ), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) ) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

Maintainer: Hajk-Georg Drost <hgd23 at cam.ac.uk>

Author(s): Hajk-Georg Drost

Install package and any missing dependencies by running this line in your R console:

install.packages("biomartr")

Depends R (>= 3.1.1)
Imports biomaRt, Biostrings, curl, tibble, jsonlite, data.table(>=1.9.4), dplyr(>=0.3.0), readr(>=0.2.2), downloader(>=0.3), RCurl(>=1.95-4.5), XML(>=3.98-1.1), httr(>=0.6.1), stringr(>=0.6.2),
Suggests knitr(>=1.6), rmarkdown(>=0.3.3), devtools(>=1.6.1), testthat, seqinr
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Package biomartr
Materials
URL https://github.com/HajkD/biomartr
Task Views
Version 0.5.1
Published 2017-05-28
License GPL-2
BugReports https://github.com/HajkD/biomartr/issues
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks biomartr check results
Package source biomartr_0.5.1.tar.gz