Genomic Data Retrieval

This package interacts with a suite of web Application Programming Interfaces and FTP sites to perform automated genomic data retieval and annotation information retrieval.

About

To automate the retrieval process on a meta-genomic scale, this package provides useful interface functions for genomic sequence retrieval and functional annotation retrieval. The major aim of biomartr is to facilitate computational reproducibility and large-scale handling of genomic data for (meta-)genomic analyses.

In detail, biomartr aims to provide users with an easy to use framework to obtain genome, proteome, CDS, GFF (annotation), genome assembly quality, and metagenome project data. Furthermore, an interface to the Ensembl Biomart database allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as

• NCBI RefSeq

• NCBI nr

• NCBI nt

• NCBI Genbank

• NCBI nt

• Ensembl

• Ensembl Genomes

• UniProt

See also

Useful links:

• https://docs.ropensci.org/biomartr/

• https://github.com/ropensci/biomartr

• Report bugs at https://github.com/ropensci/biomartr/issues

Author

Hajk-Georg Drost hajk-georg.drost@tuebingen.mpg.de