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.
Profile →npx skills add majiayu000/claude-skill-registry --skill 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.
# Metabolomics Pathway Mapping ## 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' # Pathway analysis mSet <- SetKEGG.PathLib(mSet, 'hsa', 'current') mSet <- SetMetabolomeFilter(mSet, FALSE) mSet <- CalculateOraScore(mSet, 'rbc', 'hyperg') # Over-representation # Get results pathway_results <- mSet$analSet$ora.mat print(pathway_results) ``` ## Quantitative Enrichment Analysis (QEA) ```r # For continuous data (fold changes or concentrations) mSet <- InitDataObjects('conc', 'pathqea', FALSE) mSet <- SetOrganism(mSet, 'hsa') # Load data with values metabolite_data <- data.frame( compound = c('Glucose', 'Lactate', 'Pyruvate'), fc = c(1.5, 2.3, 0.7) # Fold changes ) mSet <- Setup.MapData(mSet, metabolite_data) mSet <- CrossReferencing(mSet, 'name') # QEA analysi
- 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 majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.