jotsetung/ensembldb: Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Getting started

Package details

AuthorJohannes Rainer <> with contributions from Tim Triche, Sebastian Gibb, Laurent Gatto and Christian Weichenberger.
Bioconductor views AnnotationData Coverage Genetics Sequencing
MaintainerJohannes Rainer <>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
jotsetung/ensembldb documentation built on June 19, 2022, 4:48 p.m.