SCI Skills

EN Index
Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
BI

bio-pathway-wikipathways

Maintainer FreedomIntelligence · Last updated April 1, 2026

WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.

OpenClawNanoClawAnalysisReproductionbio-pathway-wikipathways🧬 bioinformatics (gptomics bio-* suite)bioinformatics — pathway & network analysiswikipathways

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pathway-wikipathways

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • gene_list <- de_results$log2FoldChange names(gene_list) <- de_results$entrez_id gene_list <- sort(gene_list, decreasing = TRUE).
  • gsea_wp <- gseWP( geneList = gene_list, organism = 'Homo sapiens', pvalueCutoff = 0.05, pAdjustMethod = 'BH' ).
  • head(as.data.frame(gsea_wp)).
  • wp_readable <- setReadable(wp_result, OrgDb = org.Hs.eg.db, keyType = 'ENTREZID').

Source Doc

Excerpt From SKILL.md

Core Pattern - Over-Representation Analysis

Goal: Identify WikiPathways that are over-represented in a gene list.

Approach: Test for enrichment using enrichWP against community-curated open-source pathway definitions.

"Run pathway enrichment against WikiPathways" → Test whether genes from community-curated WikiPathways are over-represented among significant genes.

Prepare Gene List

Goal: Extract significant Entrez gene IDs from DE results for WikiPathways enrichment.

Approach: Filter by significance thresholds and convert gene symbols to Entrez IDs with bitr.

GSEA on WikiPathways

Goal: Detect coordinated expression changes in WikiPathways using a ranked gene list.

Approach: Sort genes by fold change and run gseWP for rank-based enrichment testing.

Use cases

  • Use when analyzing gene lists against community-curated open-source pathways.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • go-enrichment - Gene Ontology enrichment
  • kegg-pathways - KEGG pathway enrichment
  • reactome-pathways - Reactome pathway enrichment
  • gsea - Gene Set Enrichment Analysis
  • enrichment-visualization - Visualization functions

Related skills

Related skills

Back to directory
AG
Data & ReproBioinformatics & Genomics

agent-browser

Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
AL
Data & ReproBioinformatics & Genomics

alpha-vantage

Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.

Claude CodeAnalysis
K-Dense-AI/claude-scientific-skillsView
BI
Data & ReproBioinformatics & Genomics

bio-alignment-filtering

Filter alignments by flag, quality, region, or paired status.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & ReproBioinformatics & Genomics

bio-alignment-indexing

Index BAM/CRAM files with samtools index for random access.

OpenClawNanoClawAnalysis
FreedomIntelligence/OpenClaw-Medical-SkillsView