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: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=biomartr to link to this page.
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