BgeeDB
Bioc currentAnnotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
44 13 exported
Complexity
7.9 avg / 50 max
Call network
44 nodes / 59 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
4,151
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
14
Internal functions
30
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
28.6%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-09-02
Latest release
2026-04-29
Avg cadence
179 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 15
- Examples that run
- 100%15 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 71%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/bgeedb/bgeedb_r on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| geneList | factor | 3,005 elements | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People (from the free-text Author field)
- Andrea Komljenovic author maintainer
- Julien Roux author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("BgeeDB")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkaa793.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.