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

Johannes Rainer; Laurent Gatto; Christian X Weichenberger

doi:10.1093/bioinformatics/btz031

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

Bioinformatics. 2019 Sep 1;35(17):3151-3153. doi: 10.1093/bioinformatics/btz031.

Authors

Johannes Rainer¹, Laurent Gatto², Christian X Weichenberger¹

Affiliations

¹ Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
² de Duve Institute, UCLouvain, Brussels, Belgium.

Abstract

Summary: 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.

Availability and implementation: ensembldb is part of Bioconductor (https://bioconductor.org/packages/ensembldb).

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Exons
Genome*
Molecular Sequence Annotation
Software*