biomartr: Genomic Data Retrieval

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) <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.

Version: 0.4.0
Depends: R (≥ 3.1.1)
Imports: biomaRt, Biostrings, stringi, 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
Published: 2017-03-14
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23 at cam.ac.uk>
BugReports: https://github.com/HajkD/biomartr/issues
License: GPL-3
URL: https://github.com/HajkD/biomartr
NeedsCompilation: yes
Citation: biomartr citation info
Materials: README NEWS
CRAN checks: biomartr results

Downloads:

Reference manual: biomartr.pdf
Vignettes: Ensembl BioMart Examples
NCBI Database Retrieval
Functional Annotation
Introduction
Meta-Genome Retrieval
Sequence Retrieval
Package source: biomartr_0.4.0.tar.gz
Windows binaries: r-devel: biomartr_0.4.0.zip, r-release: biomartr_0.4.0.zip, r-oldrel: biomartr_0.4.0.zip
OS X Mavericks binaries: r-release: biomartr_0.4.0.tgz, r-oldrel: biomartr_0.4.0.tgz
Old sources: biomartr archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=biomartr to link to this page.