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.
| Version: | 0.3.0 |
| 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 |
| Published: | 2017-02-09 |
| 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 |
| Reference manual: | biomartr.pdf |
| Vignettes: |
NCBI Database Retrieval Evolutionary Transcriptomics using biomartr Functional Annotation Introduction Meta-Genome Retrieval Sequence Retrieval |
| Package source: | biomartr_0.3.0.tar.gz |
| Windows binaries: | r-devel: biomartr_0.3.0.zip, r-release: biomartr_0.3.0.zip, r-oldrel: biomartr_0.3.0.zip |
| OS X Mavericks binaries: | r-release: biomartr_0.3.0.tgz, r-oldrel: biomartr_0.3.0.tgz |
| Old sources: | biomartr archive |
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