biomartr: Genomic Data Retrieval

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.

Version:	0.9.2
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), purrr, R.utils, philentropy, fs (≥ 1.3.1)
Suggests:	knitr (≥ 1.6), rmarkdown (≥ 0.3.3), devtools (≥ 1.6.1), testthat, seqinr, magrittr
Published:	2020-01-10
Author:	Hajk-Georg Drost [aut, cre]
Maintainer:	Hajk-Georg Drost <hajk-georg.drost at tuebingen.mpg.de>
BugReports:	https://github.com/ropensci/biomartr/issues
License:	GPL-2
URL:	https://docs.ropensci.org/biomartr, https://github.com/ropensci/biomartr
NeedsCompilation:	yes
Citation:	biomartr citation info
Materials:	README NEWS
CRAN checks:	biomartr results

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