{
  "id": "skill_61c2b524c9bf4f48ba0da09d1e44e4bd",
  "name": "serum-proteomics-treatment-response",
  "description": "Full pipeline for DIA-MS serum/plasma proteomics in longitudinal treatment-response studies. Covers MNAR (missing-not-at-random) protein detection via Fisher exact test, Wilcoxon differential expression for small discovery cohorts (n=8–20 per group), mixed-effects longitudinal modelling (protein ~ time × response_group + covariates), clinical score trajectory clustering (DTW + Ward.D2 hierarchical), and Tier 1/2/3 biomarker ranking with mechanistic annotation (SAM/HPA/ECM/APO axes). Psoriasis-focused with PASI trajectory clustering and MMIP responder logic, but parameterisable for any skin or immune-mediated disease. Use this skill when you have serum proteomics with ≥2 timepoints, ≥2 response groups, and want to identify pre-treatment biomarkers (MNAR pattern), mid-treatment inflammatory surge markers (T2 reactogenicity), and ranked ELISA validation candidates. Complements proteomics-diff-exp (upstream PSM aggregation), lasso-biomarker-panel (downstream panel selection), and functional-enrichment-from-degs (pathway enrichment).",
  "category": "general",
  "owner_type": "user",
  "created_by_name": "Fang Wan",
  "verified": false,
  "icon": "flask",
  "keywords": [],
  "default_message": "",
  "created_at": "2026-05-10T02:55:45.083000",
  "updated_at": "2026-06-02T00:55:40.879000",
  "entrypoint": "SKILL.md",
  "supporting_files": {
    "references/method-notes.md": {
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    "scripts/01_mnar_detection.R": {
      "type": "R",
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    },
    "scripts/02_wilcoxon_de.R": {
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    "scripts/03_longitudinal_lme.R": {
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    "scripts/04_trajectory_clustering.R": {
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    },
    "scripts/05_biomarker_tiering.R": {
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    "scripts/06_export_results.R": {
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  },
  "_category_display": "General"
}