bio-metabolomics-pathway-mapping
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-pathway-mapping --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: ReactomePA 1.46+, clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metabolomics Pathway Mapping **"Map my metabolites to pathways"** → Perform pathway enrichment and topology analysis using KEGG, Reactome, or MetaboAnalyst to interpret metabolomics results in biochemical context. - R: `MetaboAnalystR::SetMetabolomeFilter()` → `PerformDetailMatch()` → pathway topology ## KEGG Pathway Enrichment ```r library(MetaboAnalystR) # Initialize MetaboAnalyst mSet <- InitDataObjects('conc', 'pathora', FALSE) # Set organism mSet <- SetOrganism(mSet, 'hsa') # Human # Load metabolite list (HMDB IDs or compound names) metabolites <- c('HMDB0000001', 'HMDB0000005', 'HMDB0000010') # Example HMDB IDs # Or use names: c('Glucose', 'Lactate', 'Pyruvate') mSet <- Setup.MapData(mSet, metabolites) mSet <- CrossReferencing(mSet, 'hmdb') # Or 'name', 'kegg', 'pubchem'
- Version Compatibility
- KEGG Pathway Enrichment
- Quantitative Enrichment Analysis (QEA)
- Topology-Based Analysis
- Reactome Pathways
- KEGG Mapper (Direct API)
- Pathway Visualization
- Network-Based Analysis
- Metabolite Set Enrichment
- Combine with Gene Expression
- Export Results
- Related Skills
What does the bio-metabolomics-pathway-mapping skill do?
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-metabolomics-pathway-mapping --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.