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', 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. with only one command.
| Version: | 1.0.7 |
| Depends: | R (≥ 3.1.1) |
| Imports: | biomaRt, Biostrings, curl, tibble, jsonlite, data.table (≥ 1.9.4), dplyr (≥ 0.3.0), readr (≥ 1.4.0), 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, withr, fs |
| Suggests: | knitr (≥ 1.6), rmarkdown (≥ 0.3.3), devtools (≥ 1.6.1), testthat, seqinr, magrittr |
| Published: | 2023-12-02 |
| DOI: | 10.32614/CRAN.package.biomartr |
| Author: | Hajk-Georg Drost 
[aut, cre],
Haakon Tjeldnes [aut, ctb] |
| 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 |
| In views: | Omics |
| CRAN checks: | biomartr results |
Documentation:
| Reference manual: | biomartr.pdf |
| Vignettes: |
Ensembl BioMart Examples NCBI Database Retrieval Functional Annotation with biomartr Meta-Genome Retrieval Sequence Retrieval |
Downloads:
| Package source: | biomartr_1.0.7.tar.gz |
| Windows binaries: | r-devel: biomartr_1.0.7.zip, r-release: biomartr_1.0.7.zip, r-oldrel: biomartr_1.0.7.zip |
| macOS binaries: | r-release (arm64): biomartr_1.0.7.tgz, r-oldrel (arm64): biomartr_1.0.7.tgz, r-release (x86_64): biomartr_1.0.7.tgz, r-oldrel (x86_64): biomartr_1.0.7.tgz |
| Old sources: | biomartr archive |
Reverse dependencies:
| Reverse imports: | ORFik |
| Reverse suggests: | disprose, packFinder |
Linking:
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