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metabolomics-pipeline

separate

Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics, background-aware pathway mapping), naming what each stage decides and where it silently fails. Use when running a full LC-MS metabolomics study from raw mzML to enriched pathways and needing the honest handoffs between stages. Each stage defers to its component skill for parameters and traps; for stable-isotope flux (a separate branch, not this untargeted flow) see metabolomics/isotope-tracing.

When to use

• untargeted LC-MS metabolomics pipeline
• xcms 4.x feature extraction
• QC/drift/normalization
• confidence-stratified annotation
• permutation-validated statistics
• background-aware pathway mapping
• full LC-MS metabolomics study from raw mzML to enriched pathways

When not to use

• stable-isotope flux
• isotope-tracing

Skill page

Source