biomartr

swMATH19298CRANbiomartrMaRDI QIDQ31128FDOQ31128

Genomic Data Retrieval

Haakon Tjeldnes, Hajk-Georg Drost

Last update: 2 December 2023

Copyright license: GNU General Public License, version 2.0

Software version identifier: 1.0.2, 1.0.3, 0.0.1, 0.0.2, 0.0.3, 0.1.0, 0.2.0, 0.2.1, 0.3.0, 0.4.0, 0.5.1, 0.5.2, 0.7.0, 0.8.0, 0.9.0, 0.9.1, 0.9.2, 1.0.4, 1.0.5, 1.0.6, 1.0.7

Source code repository: https://github.com/cran/biomartr

Description

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.

Cites work

• BioMart – biological queries made easy
• NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
• GenBank

Cited In (1)

• GeSciLiVis

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