recipe bioconductor-ensembldb

Utilities to create and use Ensembl-based annotation databases







biotools: ensembldb, doi: 10.1038/nmeth.3252

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.

package bioconductor-ensembldb

(downloads) docker_bioconductor-ensembldb


2.12.1-0, 2.10.0-0, 2.8.0-1, 2.6.3-0, 2.4.1-0, 2.2.2-0, 2.2.0-0, 2.0.4-0, 1.6.2-0, 1.6.0-0

Required By


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-ensembldb

and update with:

conda update bioconductor-ensembldb

or use the docker container:

docker pull<tag>

(see bioconductor-ensembldb/tags for valid values for <tag>)