# YuLab-SMU/clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

Repository: https://github.com/YuLab-SMU/clusterProfiler
Canonical: https://ross.abutalabs.com/products/clusterprofiler
Homepage: https://yulab-smu.top/biomedical-knowledge-mining-book/
Language: R
License Family: other
Topics: go, kegg, enrichment-analysis, gsea, visualization, rstats
Last push: 2026-08-14T15:14:51+00:00

## Health v2 (maintenance only)
Score: 76/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 97, release rhythm 35, longevity 100
- inputs: {"age_days": 4477, "days_push": 19, "days_rel": null, "gap_med": null, "n_releases_24m": 0}
- flags: no_releases, no_license
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1226, forks 267 (observed 2026-08-28T04:04:03.155820+00:00)

## What it is
An R/Bioconductor package for functional enrichment analysis (ORA, GSEA, topology-aware) of omics data across thousands of species. It provides a tidy interface to access, manipulate, and visualize enrichment results for biological interpretation.

## Use cases
- run GO and KEGG enrichment analysis on a list of differentially expressed genes
- perform GSEA on a ranked gene list from RNA-seq
- visualize enrichment results with dotplots, barplots, and enrichment maps
- compare enrichment across multiple treatments and time points in one run
- interpret functional characteristics of coding and non-coding genomics data
- do pathway enrichment analysis for multi-omics datasets

## When to choose
- you need gene set enrichment or over-representation analysis in R
- you want well-established, widely cited tooling for omics interpretation
- you need to compare enrichment results across conditions or datasets
- you want publication-quality visualization of enrichment results

## When to avoid
- you need enrichment analysis outside R or in a pipeline language like Python
- you need single-cell-specific analysis rather than bulk enrichment
- you want a web GUI rather than a programmatic R interface

## Facets
- artifact type: library
- maturity: active
- function: data-visualization, analytics, data-science
- domain: bioinformatics, data-science, data-visualization
- platform: cross-platform
- tags: enrichment-analysis, gsea, gene-ontology, kegg, omics, bioconductor, ora, pathway-analysis, r

## Member repositories
- YuLab-SMU/clusterProfiler (main) score 76

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:04:03.155820+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T06:15:18.141920+00:00, confidence not recorded.
  - readme: https://github.com/YuLab-SMU/clusterProfiler (fetched 2026-08-28T04:04:03.155820+00:00, sha 48c6f2d7ea29)
  - homepage: https://yulab-smu.top/biomedical-knowledge-mining-book/ (fetched 2026-08-29T12:23:02.666660+00:00, sha ddc39ab7f7dc)
  - site_page: https://yulab-smu.top/biomedical-knowledge-mining-book/FAQ.html (fetched 2026-08-29T12:23:02.675774+00:00, sha 8a1fd1836b17)
- Data as of 2026-08-30T08:39:29.467469+00:00.