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


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.

SUBMITTER: Rainer J 

PROVIDER: S-EPMC6736197 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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

Rainer Johannes J   Gatto Laurent L   Weichenberger Christian X CX  

Bioinformatics (Oxford, England) 20190901 17


<h4>Summary</h4>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  ...[more]

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