ensembldb
Bioc currentUtilities to create and use Ensembl-based annotation databases
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
147 38 exported
Complexity
4.8 avg / 30 max
Call network
147 nodes / 128 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
21,604
Files
99
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
40
Internal functions
109
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.61
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
7.7%
Unsafe pattern score
2
Dep constraint coverage
61.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
LGPL
License flags
not SPDX, not OSI
History
Versions
23
First release
2015-06-11
Latest release
2026-05-25
Avg cadence
180 days
Cold removal rate
100%
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 26
- Examples that run
- 96%23 run in a plain check · 1 never run
- Exported functions with examples
- 88%
- Documented parameters
- 100%
- Return-value docs
- 94%
- Help pages citing references
- 0%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/jorainer/ensembldb on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2023-02-23 · The repository has a site deploy workflow
Topics
Depended on by (47)
Show 55 packagesHide 55 packages
Bioconductor (43)
CRAN (4)
People
- Johannes Rainer author maintainer
- Laurent Gatto contributor
- Sebastian Gibb contributor
- Tim Triche contributor
- Christian Weichenberger contributor
- Boyu Yu contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("ensembldb")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btz031.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.