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: | 0.7.0 |
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 |
Published: | 2018-01-03 |
Author: | Hajk-Georg Drost |
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 |
Reference manual: | biomartr.pdf |
Vignettes: |
Ensembl BioMart Examples NCBI Database Retrieval Functional Annotation Introduction Meta-Genome Retrieval Sequence Retrieval |
Package source: | biomartr_0.7.0.tar.gz |
Windows binaries: | r-devel: biomartr_0.7.0.zip, r-release: biomartr_0.7.0.zip, r-oldrel: biomartr_0.7.0.zip |
OS X El Capitan binaries: | r-release: not available |
OS X Mavericks binaries: | r-oldrel: biomartr_0.7.0.tgz |
Old sources: | biomartr archive |
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