ensembldb: an R package to create and use Ensembl-based annotation resources.

Abstract

Bioinformatics research frequently involves handling gene-centric data such as exons, transcripts, proteins and their positions relative to a reference coordinate system. The ensembldb Bioconductor package retrieves and stores Ensembl-based genetic annotations and positional information, and furthermore offers identifier conversion and coordinates mappings for gene-associated data. In support of reproducible research, data are tied to Ensembl releases and are kept separately from the software. Premade data packages are available for a variety of genomes and Ensembl releases. Three examples demonstrate typical use cases of this software. ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb). Supplementary data are available at Bioinformatics online.