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

Johannes Rainer | Zendy; Laurent Gatto | Zendy; Christian X. Weichenberger | Zendy

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

Author(s) -

Johannes Rainer,

Laurent Gatto,

Christian X. Weichenberger

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz031

Subject(s) - ensembl , bioconductor , identifier , computer science , software , annotation , gene nomenclature , r package , software package , data mining , computational biology , genome , bioinformatics , information retrieval , genomics , biology , gene , genetics , programming language , artificial intelligence , taxonomy (biology) , botany , nomenclature

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.

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