toppgene
Bioc currentGene List Enrichment Analysis using the ToppGene Suite
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
The ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. Although the ToppCluster web application provides convenient graphical access to the ToppGene Suite, the OpenAPI 3.0 compliant interface of ToppGene is better suited for automation and reproducibility. This package includes Bioconductor class interfaces and biological examples.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 4 exported
Complexity
2.2 avg / 9 max
Call network
29 nodes / 27 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
1,687
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
25
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.45
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.6.0
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-30
Latest release
2026-04-30
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Pariksheet Nanda author maintainer
- Jason Shoemaker fnd
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("toppgene")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-08, which the citation names so these numbers can be found later. More on citing and the projects behind them.