Package: biomartr
Title: Genomic Data Retrieval
Version: 0.3.0
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Description: 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' (Yates et al. (2016) <doi:10.1093/nar/gkv1157>) 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. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
VignetteBuilder: knitr
NeedsCompilation: yes
Depends: R (>= 3.1.1)
Imports: biomaRt, Biostrings, stringi, 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
License: GPL-3
LazyData: true
URL: https://github.com/HajkD/biomartr
BugReports: https://github.com/HajkD/biomartr/issues
RoxygenNote: 6.0.1
Encoding: UTF-8
Packaged: 2017-02-09 17:32:28 UTC; h-gd
Repository: CRAN
Date/Publication: 2017-02-09 19:59:35
