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 ORCID iD [aut, cre], Haakon Tjeldnes [aut, ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost at>
License: GPL-2
NeedsCompilation: yes
Citation: biomartr citation info
Materials: README NEWS
In views: Omics
CRAN checks: biomartr results


Reference manual: biomartr.pdf
Vignettes: Ensembl BioMart Examples
NCBI Database Retrieval
Functional Annotation with biomartr
Meta-Genome Retrieval
Sequence Retrieval


Package source: biomartr_1.0.7.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
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


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