ensembldb: an R package to create and use Ensembl-based annotation resources.
(2019) Bioinformatics (Oxford, England) — Vol. 35, n° 17, p. 3151-3153 (2019)
Files
btz031.pdf
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Open Access - Adobe PDF
- 499.77 KB
Details
- Authors
- 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.
- Affiliations
Citations
Rainer, J., Gatto, L., & Weichenberger, C. X. (2019). ensembldb: an R package to create and use Ensembl-based annotation resources. Bioinformatics (Oxford, England), 35(17), 3151-3153. https://doi.org/10.1093/bioinformatics/btz031 (Original work published 2019)