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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "ensembldb" in publications use:'
type: software
license: LGPL-2.0-only
title: 'ensembldb: Utilities to create and use Ensembl-based annotation databases'
version: 2.36.1
doi: 10.1093/bioinformatics/btz031
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ensembldb
abstract: 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.
authors:
- family-names: Rainer
  given-names: Johannes
  email: johannes.rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147
preferred-citation:
  type: article
  title: 'ensembldb: an R package to create and use Ensembl-based annotation resources.'
  authors:
  - family-names: Rainer
    given-names: Johannes
    email: johannes.rainer@eurac.edu
    orcid: https://orcid.org/0000-0002-6977-7147
  - family-names: Gatto
    given-names: Laurent
  - family-names: Weichenberger
    given-names: Christian X.
  year: '2019'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btz031
  url: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz031/5301311
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/jorainer/ensembldb
commit: 5c98c2bf9b076b963d13d136ba7631668b8a1db2
url: https://github.com/jorainer/ensembldb
date-released: '2026-05-25'
contact:
- family-names: Rainer
  given-names: Johannes
  email: johannes.rainer@eurac.edu
  orcid: https://orcid.org/0000-0002-6977-7147