ensembldb: an R package to create and use Ensembl-based annotation resources
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 …
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 …
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.
Oxford University Press