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.
None published for Bioconductor
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
1,688
Files
25
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
25
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.45
testthat edition
3
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
2026-08-03
Latest release
2026-08-03
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
- Help pages
- 5
- Examples that run
- 100%4 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- toppgene HTML
Bug fixes and improvements
- Backport fixes from 1.1.2 for
CategoriesDataFramedispatch ofsubset()method (24c42a9) and for git repo ownership forBiocCheck()during GitHub Actions (9659a0c).
From NEWS.md in the release
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/immusystems-lab/toppgene on 2026-10-22.
The R CMD check workflow runs on Linux, and on R-devel
Topics
People
- Pariksheet Nanda author maintainer
- Jason Shoemaker funder
Cite
Cite this package
Run in R for the authors' entry:
citation("toppgene")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/1471-2105-8-392, 10.1093/nar/gkq418.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.