YuLab-SMU/clusterProfiler

Health v2 · maintenance only

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Adoption not part of the score

1226 stars · 267 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

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

library · maturity active

data-visualization analytics data-science bioinformatics data-science data-visualization cross-platform enrichment-analysis gsea gene-ontology kegg omics bioconductor ora pathway-analysis r

Member repositories

For agents

markdown · JSON · MCP: product_card(name="YuLab-SMU/clusterProfiler")