OncoPath

Oncology-specific templates: staging, response assessment, biomarkers, and molecular summaries

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What it does

OncoPath is the oncology-specific layer on top of ClinicoPathJamoviModule. It handles the analyses and summaries that are specific to cancer studies:

  • Staging — AJCC/UICC TNM summaries, stage-migration analyses, grouped-stage comparisons.
  • Treatment response — RECIST / response rate summaries, waterfall and swimmer plots.
  • Biomarkers — cut-point analysis, categorization (tertiles, quartiles, ROC-derived), biomarker × outcome tables.
  • Molecular features — mutation / co-mutation matrices, oncoprint-style plots.
  • Subgroup / forest summaries — treatment effect by subgroup with consistent formatting.

When to use

  • The paper is an oncology study (resection outcomes, neoadjuvant response, biomarker validation, drug-response series).
  • You need consistent TNM summaries that automatically apply the right edition.
  • You need a waterfall, swimmer, or oncoprint plot without hand-coding.

Repos

Quick start in jamovi

  1. Analyses → ClinicoPath → OncoPath → TNM summary.
  2. Supply T, N, M columns (coded) and the edition (AJCC 7 / 8).
  3. Get a stage-grouped table and a migration matrix to prior editions.

For response analyses:

  1. Analyses → ClinicoPath → OncoPath → Response → Waterfall.
  2. Supply the best-response percent change and optional response category.
  3. Plot includes the ±20 / ±30 RECIST lines by default.

Pitfalls

  • Edition matters. AJCC 7 and AJCC 8 disagree on substantial numbers of cases. State the edition explicitly in every table; the module forces this in the caption.
  • Waterfall ordering. Reviewers will want the waterfall ordered by percent change, not by ID. The module does that by default — don’t override.
  • Biomarker cut-points. Data-derived cut-points overfit unless validated. Use the module’s split-sample or cross-validated cut-point option; document the method.