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bio-pathway-w Wikipathways

Identify enriched WikiPathways from gene lists using clusterProfiler and rWikiPathways.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Analyzes gene lists to identify enriched WikiPathways, enabling interpretation of biological signals with community-curated pathway knowledge.

Core Features & Use Cases

  • Over-representation analysis using enrichWP against WikiPathways definitions for 30+ species.
  • Gene Set Enrichment Analysis (GSEA) with gseWP on ranked gene lists.
  • Supports multiple organisms and ID conversion workflows to produce readable results for downstream reporting.

Quick Start

Run WikiPathways enrichment on a list of Entrez IDs or gene symbols to discover enriched pathways and generate plots.

Frequently Asked Questions about bio-pathway-w Wikipathways

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

FAQPage Schema
How do I perform WikiPathways enrichment analysis on a gene list using R?▼

WikiPathways enrichment analysis identifies over-represented pathways in a gene list using clusterProfiler and rWikiPathways. You can run ORA with enrichWP or GSEA with gseWP on Entrez IDs or gene symbols to discover enriched biological pathways.

Can I use clusterProfiler for GSEA on a ranked gene list with WikiPathways?▼

Yes, clusterProfiler supports GSEA on ranked gene lists with WikiPathways using the gseWP function. This allows you to identify enriched pathways from differential expression results without setting an arbitrary gene significance threshold.

Does WikiPathways enrichment support model organisms other than humans?▼

WikiPathways enrichment supports over 30 species, enabling pathway analysis for various model organisms. The workflow integrates with rWikiPathways and allows ID conversion workflows to produce readable results for your specific organism.

What input format is required for gene list pathway analysis with rWikiPathways?▼

Gene list pathway analysis requires a list of Entrez IDs or gene symbols as input. You also need R, clusterProfiler, rWikiPathways, and org.Hs.eg.db installed, with an optional background universe gene list for more accurate enrichment results.

What is the difference between ORA and GSEA for pathway analysis?▼

ORA identifies enriched WikiPathways in a pre-defined gene list of significant genes, while GSEA calculates enrichment scores across an entire ranked gene list. Both methods use clusterProfiler functions enrichWP and gseWP to interpret biological signals.

How do I convert gene symbols to Entrez IDs for WikiPathways enrichment?▼

Gene symbol to Entrez ID conversion for WikiPathways enrichment is supported through optional ID conversion steps. The analysis requires org.Hs.eg.db and utilizes clusterProfiler workflows to map identifiers before running enrichWP or gseWP.

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