BgeeCall
Bioc currentAutomatic RNA-Seq present/absent gene expression calls generation
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
84 18 exported
Complexity
4.9 avg / 22 max
Call network
84 nodes / 126 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
9,971
Files
85
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
33
Internal functions
61
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
9.1%
Unsafe pattern score
4
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
1 externalkallisto
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-10-14
Latest release
2026-07-06
Avg cadence
168 days
Cold removal rate
100%
Dep drift
19
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 39includes a package overview page
- Examples that run
- 77%23 run in a plain check · 7 never run
- Exported functions with examples
- 91%
- Documented parameters
- 100%
- Return-value docs
- 94%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/bgeedb/bgeecall on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Topics
People
- Julien Wollbrett author maintainer
- Frederic Bastian author
- Alessandro Brandulas Cammarata author
- Sara Fonseca Costa author
- Marc Robinson Rechavi contributor
- Julien Roux author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("BgeeCall")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.