Biomartr: genomic data retrieval with R

Abstract

$\textbf{MOTIVATION}$: Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, $\textit{biomartr}$, which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses. $\textbf{RESULTS}$: The $\textit{biomartr}$ package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, $\textit{biomartr}$ communicates with the BioMartr database for functional annotation of retrieved sequences. Comprehensive documentation of $\textit{biomartr}$ functions and five tutorial vignettes provide step-by-step instructions on how to use the package in a reproducible manner. $\textbf{AVAILABILITY AND IMPLEMENTATION}$: The open source $\textit{biomartr}$ package is available at https://github.com/HajkD/biomartr and https://cran.r-project.org/web/packages/biomartr/index.htmlThis work was supported by an European Research Council grant named EVOBREED [grant number 322621] (to JP) and a Gatsby Fellowship [grant number AT3273/GLE] (to JP)