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bio-pathway-reactome

Analyzes Reactome pathway enrichment for gene lists using enrichPathway and gsePathway.

Updated Mar 30, 2026
Search Tags:#visualization#reactome#gene-list#bioconductor#pathway-enrichment#gsea#enrichPathway
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-pathway-reactome
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-pathway-reactome
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-pathway-analysis-reactome-pathways
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-pathway-reactome

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Enables researchers to identify biologically meaningful Reactome pathways that are overrepresented in a given gene list, turning raw gene data into interpretable pathway insights.

Core Features & Use Cases

  • Over-representation analysis with enrichPathway to identify enriched Reactome pathways from a gene set.
  • GSEA support using gsePathway to detect coordinated shifts in pathways across a ranked gene list.
  • Cross-species applicability supporting human and common model organisms, with visualization and browser viewing of pathways.

Quick Start

Provide your significant genes or a ranked gene list to run Reactome pathway enrichment and view the top enriched pathways.

Frequently Asked Questions about bio-pathway-reactome

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform Reactome pathway enrichment on a gene list?▼

Reactome pathway enrichment identifies overrepresented biological pathways from a gene list by using enrichPathway for over-representation analysis or gsePathway for ranked lists, generating plots and exporting results.

Can I run GSEA on a ranked gene list using Reactome pathways?▼

Yes, you can run GSEA on a ranked gene list using the gsePathway function to detect coordinated shifts in biological pathways across your ranked data and visualize the results.

Do I need Bioconductor packages to analyze Reactome pathway enrichment?▼

Yes, you need Bioconductor packages like ReactomePA and org.Hs.eg.db installed as prerequisites to execute enrichPathway and gsePathway functions for identifying enriched biological pathways.

Does Reactome pathway enrichment support model organisms other than humans?▼

Reactome pathway enrichment supports cross-species applicability for humans and common model organisms by utilizing the appropriate OrgDb packages alongside ReactomePA to identify enriched pathways.

How do I visualize enriched Reactome pathways from differential expression results?▼

You can visualize enriched Reactome pathways from differential expression results by using the viewPathway function to generate plots and view biological pathways directly in the browser.

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