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: 0.8.0
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
Suggests: knitr (≥ 1.6), rmarkdown (≥ 0.3.3), devtools (≥ 1.6.1), testthat, seqinr, magrittr
Published: 2018-06-27
Author: Hajk-Georg Drost ORCID iD [aut, cre]
Maintainer: Hajk-Georg Drost <hgd23 at cam.ac.uk>
BugReports: https://github.com/ropensci/biomartr/issues
License: GPL-2
URL: https://github.com/ropensci/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
Meta-Genome Retrieval
Sequence Retrieval
Package source: biomartr_0.8.0.tar.gz
Windows binaries: r-devel: biomartr_0.8.0.zip, r-release: biomartr_0.8.0.zip, r-oldrel: biomartr_0.8.0.zip
OS X binaries: r-release: biomartr_0.8.0.tgz, r-oldrel: biomartr_0.8.0.tgz
Old sources: biomartr archive

Reverse dependencies:

Reverse imports: myTAI

Linking:

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