clusterProfiler
Bioc currentA Universal Enrichment Tool for Interpreting Omics Data
Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
A universal tool for interpreting functional characteristics of omics data. It supports Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) for both coding and non-coding genomics data of thousands of species. It provides a unified and tidy interface to access, manipulate, and visualize enrichment results. A key capability is the simultaneous analysis and comparison of datasets from multiple treatments or time points. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
154 44 exported
Complexity
4 avg / 35 max
Call network
154 nodes / 131 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
8,202
Files
110
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
72
Internal functions
108
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
97.2%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
22.2%
Unsafe pattern score
9
Dep constraint coverage
23.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
31
First release
2011-07-29
Latest release
2026-04-28
Avg cadence
187 days
Cold removal rate
100%
Dep drift
44
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 51 (3 internal)includes a package overview page
- Examples that run
- 25%2 run in a plain check · 6 never run
- Exported functions with examples
- 18%
- Documented parameters
- 100%
- Return-value docs
- 96%
- Help pages citing references
- 2%
- clusterProfiler.html HTML
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/yulab-smu/clusterprofiler on 2026-10-22.
GitHub Pages site last deployed 2026-06-07 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DE_GSE8057 | data.frame | 1,251 × 3 | No other package |
| gcSample | list | 8 elements | No other package |
| kegg-mapper-blast | data.frame | 2,999 × 2 | No other package |
| kegg_taxa | data.frame | 7,783 × 3 | No other package |
Topics
Depended on by (63)
Show 64 packagesHide 64 packages
Bioconductor (59)
CRAN (4)
Suggested by (54)
People
- Guangchuang Yu author maintainer copyright holder
- Meijun Chen contributor
- Giovanni Dall'Olio contributor
- Chun-Hui Gao contributor
- Xiao Luo contributor
- Li-Gen Wang contributor
- Wanqian Wei contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("clusterProfiler")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1016/j.xinn.2024.100722, 10.1038/s41596-024-01020-z, 10.1016/j.xinn.2021.100141, 10.1089/omi.2011.0118.
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.