MedSci Skills

56 skills that actually work. Built by a physician-researcher, tested on real publications.

MedSci Skills is an end-to-end research tool for physician and medical-engineering researchers — design → scaffold → validate → publish — for the clinical manuscript and the medical-AI model behind it. Its moat is the compliance layer — 46 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.

License: MIT Release CI Skills npm npm downloads Watch the 2-min intro good first issues

Agent Skills Claude Code Codex Cursor GitHub Copilot

DOI arXiv Citation Built by

MedSci Skills

Topic Discovery → Literature Search → Full-Text Retrieval → Study Design → Sample Size → Protocol → De-identification → Data Cleaning → Statistics → Figures → Writing → Humanize → Compliance → Journal Selection → Peer Review → Revision → Presentation

Created & maintained by Yoojin Nam, MD Department of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea

check-reporting demo


What is MedSci Skills?

MedSci Skills is an open-source Agent Skills collection for clinical research — the manuscript and the medical-AI model alike — designed to be driven directly by AI coding agents (Claude Code, Codex, Cursor, and GitHub Copilot). It helps physician-researchers and biomedical/medical-engineering investigators move from literature search, study design, statistics, and figures to reporting-guideline compliance, citation/reference auditing, numerical-consistency checks, and response-to-reviewer workflows — combining agentic writing with deterministic integrity gates for submission-grade biomedical research. As of v5.0 it adds a model-engineering lane: choose a paper-grounded architecture, scaffold a reproducible, leakage-safe PyTorch training repo, and validate, document, and evaluate a medical-imaging or LLM/MLLM model so the work reaches a paper — it ships a minimal runnable default model for a forward-pass smoke test and integrates MONAI / nnU-Net / timm / torchvision for production-grade models, rather than reimplementing the ecosystem. Clinical AI model research engineering is in scope; it is not a diagnostic tool, an autonomous author, or a general AI-scientist platform, and every output requires human-expert verification. New here? See the 3 workflows below, the FAQ, the research connectors it calls (keyless public APIs — nothing to set up in the common case), and the scope boundary.


Quick Start

No terminal? Use the classroom installer ZIP — download, unzip, double-click the installer, then restart your agent app (see Installation).

Have a terminal? Fastest path — one command, nothing to clone:

npx medsci-skills install        # copies every skill into your agent's folder

Recommended (especially for clinicians): add --enable-update-notify so Claude Code shows a one-line "update available" notice when a new version ships — otherwise you stay on the version you installed and are never told. (No terminal at all? The classroom installer below turns this on for you.)

npx medsci-skills install --enable-update-notify        # install + in-app update reminders

Have git? Install every skill in three commands:

git clone https://github.com/Aperivue/medsci-skills.git
mkdir -p ~/.claude/skills
cp -r medsci-skills/skills/* ~/.claude/skills/

Restart Claude Code, then start with /orchestrate — it classifies your request and routes you to the right skill. Full install options (Codex, Cursor, individual skills) are in Installation.

Install as a Claude Code plugin

Prefer plugins? One line adds the marketplace; /plugin then lets you browse nine category plugins and enable the ones you want:

/plugin marketplace add Aperivue/medsci-skills
/plugin            # browse nine category plugins; enable the ones you want
Plugin Covers
medsci-literature Literature search, full-text retrieval, Zotero sync, reference-integrity audits
medsci-data Study design, variable operationalization, sample size, data cleaning, de-identification, codebooks, dataset versioning
medsci-modeling Architecture selection, reproducible model-scaffold repos, model-validation audits, Model Card/Datasheet, model & LLM/MLLM evaluation
medsci-analysis Statistics, figures, batch/cross-national/replication analysis, meta-analysis
medsci-writing IMRAD & protocol drafting, AI-pattern removal, AI-search optimization, reviewer responses
medsci-review Self-review, peer review, reporting-guideline compliance
medsci-submission Submission packaging, journal selection, ICMJE/IRB form filling, grant proposals
medsci-project Orchestration, project intake/management, gap & topic discovery, author strategy
medsci-presentation Presentations/PPTX, PDF/document rendering, environment setup, skill publishing

Install a single category and invoke its skills under that namespace:

/plugin install medsci-analysis@medsci-skills
/medsci-analysis:analyze-stats

All eight plugins share the same repository source, so this groups and enables skills by category — it is not a partial download. The marketplace tracks main, so a plugin's version is its git commit.

Want just one capability? Two skills are also published as focused standalone repos (generated mirrors; this repo stays the source of truth), each installable on its own with /plugin marketplace add Aperivue/<repo>:


Start here: 3 workflows

New users don't need all the skills at once. Most work starts as one of three workflows. Each runs through /orchestrate or by invoking the named skills in order; all outputs require human-expert review.

Workflow A — Manuscript pre-submission audit. Use when a manuscript is nearly ready and you want it checked before a reviewer sees it. Skills: /self-review/check-reporting/verify-refs/sync-submission. In: your manuscript (+ refs.bib, tables/figures). Out: anticipated reviewer comments, an item-by-item reporting-guideline audit, a citation-integrity report, and a submission-package drift check. Safety: it flags issues; you fix and verify them.

Workflow B — Data to manuscript package. Use when you have a cleaned dataset and need a full draft. Skills: /clean-data/analyze-stats/make-figures/write-paper/check-reporting/find-journal. In: a cleaned CSV/parquet

  • a research question. Out: reproducible analysis code, publication-ready figures, an IMRaD draft, a reporting checklist, and a journal shortlist. Safety: statistics and claims must be verified against your data; the toolkit never fabricates numbers or references.

Workflow C — Systematic review / meta-analysis. Use when you are running an SR/MA. Skills: /meta-analysis (with /search-lit, /make-figures, /check-reporting). In: a research question + search strategy. Out: PROSPERO-style protocol scaffolding, screening/extraction structure, PRISMA-consistent counts and diagram, pooled-estimate figures, and a manuscript draft. Safety: screening and extraction decisions stay with the human review team.

Live Demos: Four Study Types, Four Full Pipelines

Four public datasets. Four study types. Demos 1–3 each produce a complete manuscript, publication-ready figures, and a reporting-compliance audit; Demo 4 runs the medical-AI model-engineering lane end to end (scaffold → gates → training → evaluation → interpretability).

Demo Dataset Study Type Compliance
Demo 1: Wisconsin BC sklearn built-in Diagnostic accuracy STARD 2015
Demo 2: BCG Vaccine metafor::dat.bcg (13 RCTs) Meta-analysis PRISMA 2020
Demo 3: NHANES Obesity CDC NHANES 2017-18 Epidemiology (survey) STROBE
Demo 4: PneumoniaMNIST CNN medmnist (CC BY 4.0) Medical-AI model engineering (CNN) CLAIM / TRIPOD+AI

Demo 1: Diagnostic Accuracy — Wisconsin Breast Cancer

from sklearn.datasets import load_breast_cancer
data = load_breast_cancer()  # 569 samples, zero download

Output from orchestrate --e2e (see full demo):

Output Description
Manuscript IMRAD draft, ~1,800 words
Title Page STARD title page with key points
DOCX Submission-ready Word document
ROC Curve 3-model comparison with DeLong 95% CIs
Confusion Matrices Per-model confusion matrices at threshold 0.5
STARD Flow D2-generated STARD 2015 flow diagram
Reporting Checklist STARD 2015 — 60.9% compliance (14/23 applicable)
Self-Review Initial 82 (REVISE) → 88 (PASS) after 1 fix iteration; final 0 major / 1 minor
Pipeline Log 7-step E2E execution trace

Pipeline: analyze-statsmake-figureswrite-paper → AI pattern scan → check-reporting (STARD) → self-review → DOCX build → present-paper

Demo 2: Meta-Analysis — BCG Vaccine Efficacy

library(metafor)
data(dat.bcg)  # 13 RCTs, 357,347 participants (Colditz et al. 1994)

Output from orchestrate --e2e (see full demo):

Output Description
Manuscript Pooled RR = 0.489 (95% CI: 0.344–0.696), ~2,200 words
Title Page PRISMA title page with key points
DOCX Submission-ready Word document
Forest Plot 13 studies, RE model (REML), 300 dpi
Funnel Plot Small-study / publication-bias visual
PRISMA Flow D2-generated PRISMA 2020 flow diagram
Reporting Checklist PRISMA 2020 — 57.1% (24/42) at check-reporting → 61.9% (26/42) after self-review fix
Self-Review Initial 78 → 82 (REVISE) after 1 fix iteration; 3 major / 4 minor (majors are out-of-scope RoB/GRADE/references)
Pipeline Log 7-step E2E execution trace

Pipeline: analyze-stats (R metafor) → make-figureswrite-paper → AI pattern scan → check-reporting (PRISMA 2020) → self-review → DOCX build → present-paper

Demo 3: Epidemiology — NHANES Obesity & Diabetes

# Pre-processed NHANES 2017-2018 CSV included
# 5,010 US adults after exclusions

Output from orchestrate --e2e (see full demo):

Output Description
Manuscript Adjusted OR = 3.03 (95% CI: 2.29–4.02), ~1,850 words
Title Page STROBE title page with key points
DOCX Submission-ready Word document
OR Forest Plot Adjusted odds ratios for 7 variables
Study Flow D2-generated participant flow diagram
Reporting Checklist STROBE — 83.3% compliance (25/30 applicable)
Self-Review ACCEPT-WITH-NOTES after 1 fix iteration; 0 genuine majors remaining
Pipeline Log 7-step E2E execution trace

Pipeline: analyze-statsmake-figureswrite-paper → AI pattern scan → check-reporting (STROBE) → self-review → DOCX build → present-paper

Project Folder Structure

Each demo (and real project) follows this role-based folder layout:

project/
├── data/                          # Input data
│   └── raw_data.csv
├── analysis/                      # /analyze-stats + /make-figures outputs
│   ├── tables/
│   ├── figures/
│   │   └── _figure_manifest.md
│   ├── _analysis_outputs.md
│   └── analyze.py
├── manuscript/                    # /write-paper outputs
│   ├── manuscript.md
│   ├── manuscript_final.docx
│   └── title_page.md
├── qc/                            # Quality verification
│   ├── reporting_checklist.md     # /check-reporting
│   ├── self_review.md             # /self-review
│   └── _pipeline_log.md
├── submission/                    # Post-journal-selection (manual trigger)
│   └── {journal_short}/
│       ├── cover_letter.md
│       ├── checklist.md
│       └── peer_review.md
└── presentation/
    └── presentation.pptx

The E2E pipeline (orchestrate --e2e) produces everything up to qc/. The submission/ directory is created after journal selection via /find-journal.


What's New

v5.21 — verification-layer batch, mostly promoted from real submission failures. A marked (tracked-changes) manuscript is now built by driving Word's Compare from the command line and proved by a round trip — accepting every revision must reproduce the revised paper exactly, rejecting every revision must reproduce the original — and the gate is move-aware, because Word encodes a relocated paragraph as w:moveFrom/w:moveTo and an insert-and-delete-only verifier calls a good file corrupt. Every detector's qc/*.json now names the detector that wrote it, so an artifact can be traced back to the check that produced it (a CI-enforced contract). Two /verify-refs precision defects: a Unicode hyphen in a surname fired MISMATCH — the verdict that means fabricated author — on a correct reference, and a Better BibTeX brace-protected surname was read as a corporate author, silently skipping the author check the tool exists to perform. New gates: publisher markup in a .bib title (<scp>WHO</scp> renders as garbage and no gate looked at the printed title), complete/quasi separation before a logistic model is fitted (a pathognomonic sign has an empty cell by construction; glm returns OR = 0.00, p = 0.99, and an AUC that gets reported), and a probe + gate for manuscripts claiming a system improved itself (which rung of the verification hierarchy said so?). /find-cohort-gap now accepts a local codebook — an institutional registry or EMR export, not only a named public cohort — enumerating variables verbatim with provenance rather than letting a model summarise them. Additive and backward-compatible; 55 skills / 46 guidelines / 61 integrity detectors / 23 domain-probe modules. (See the CHANGELOG for v5.0–v5.20.)

v5.20.1 — audit-driven coherence fixes. A real /orchestrate --e2e state-transition bug (the pipeline halted at step 3 because it required a DOCX that is only rendered at step 7), all 55 skills made routable from the single entry point with a CI reachability gate, and a README plugin-count that had drifted from the marketplace SSOT (now gated). No skill/detector change.

v5.20 — reviewer-arithmetic gates. Five deterministic self-review detectors promoted from a peer-review cycle, each recomputing what a manuscript already prints: check_table_percentages (an n (%) cell vs its column denominator), check_nested_group_comparison (a P value comparing an analysed subset against the parent cohort that contains it — nested, invalid), check_reported_p_from_counts (rebuilds each 2×2 row and recomputes Fisher / Pearson χ² ± Yates in pure stdlib, calibrating the family on rows that reproduce), check_dta_denominators (sensitivity/specificity denominators vs the reference-standard category counts, behind a matching grand total), and check_paired_difference_estimator (an odd-n integer-scale median cannot be non-integer; a zero-width CI; an unnamed estimator). Plus /peer-review request-type discipline (disclosure vs computation) and impossibility-claim verification. Additive and backward-compatible; 55 skills / 46 guidelines / 57 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.19.)

v5.19 — reviewer-safety + reporting-checklist batch. A PDF hidden-text / prompt-injection guard for /peer-review — a PyMuPDF extractor plus a stdlib detector that catch a review-steering instruction hidden in a submitted PDF (white-on-white text, sub-visible fonts, off-page glyphs, invisible render mode, or a document-metadata field) before an LLM ingesting the text layer can be steered by it, and emit visible-only text to feed a model instead of the raw PDF; plus the TARGET (target-trial emulation; Cashin et al., JAMA 2025) and REMARK (prognostic tumour-marker; McShane et al.) reporting checklists. Additive and backward-compatible; 55 skills / 46 guidelines / 52 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.18.)

v5.18 — reliability & workflow-integrity batch. A new deterministic response-claim gate for /revise and /peer-review (verifies a response letter's "we added / we now cite X" against the revised manuscript body — a claimed-but-absent edit is caught before it reaches a reviewer; detectors 50 → 51), a reframe / headline-change survivor scan (--retired-term / --old-value, finds stale framing or superseded values left in the body, supplement, and figure legends after a reframe), a pre-drafting backbone full-text readiness gate for /write-paper (the backbone article is used, not merely detected), a skill-registry consistency validator (capabilities.ymlskill.yml, CI-enforced), AI-tool citation-framing guidance for /academic-aio, and Demo 4 (PneumoniaMNIST CNN, the model-engineering lane end to end). Additive and backward-compatible; 55 skills / 46 guidelines / 51 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.17.)

v5.17 — model-engineering produce-side depth, completion. Deployment safety + the final roadmap/candidate items: a new uncertainty-imaging skill + check_uncertainty_reporting gate (calibrated per-case uncertainty / OOD guard on a held-out set / abstention at a pre-specified target / calibration-under-shift — for a deployment-framed model), an MLOps wiring reference for model-scaffold (experiment tracking, config/data/environment versioning, CI-for-ML — pointing to W&B / MLflow / nnU-Net, reimplementing nothing), and an architecture-zoo graph-neural-net family card (GCN / GraphSAGE / GAT / GIN / BrainGNN for brain connectomes) that closes the last candidate gap. The six-item produce-side depth roadmap and its candidate list are now complete. Additive and backward-compatible; 55 skills / 46 guidelines / 50 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.16.)

v5.16 — model-engineering produce-side depth, clinical fine-tuning focus (Items 3–4 of the produce-side depth roadmap). A new radiomics-ml skill + check_radiomics_ml gate for the most common solo-doable clinical-ML workflow — radiomics / tabular features → any classical learner (LASSO / SVM / random forest / XGBoost / …) → a clinical outcome, no GPU — with a learner-agnostic nested-CV / calibration / stability gate; plus a model-scaffold fine-tuning mode (--task finetune + --from-pretrained) that adapts a pretrained backbone on collected clinical data with a frozen→unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record (PRETRAINED.md + a PRETRAINED_PROVENANCE_MISSING verdict on the existing check_training_hygiene, plus a MedSAM-adaptation + train-only diffusion-augmentation guide). Additive and backward-compatible; 54 skills / 46 guidelines / 49 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.15.)

v5.15 — model-engineering produce-side depth. Two new skills that produce what the review lane previously only audited: preprocess-imaging (DICOM/NIfTI data prep + a check_preprocessing_leakage gate that extends the split-leakage moat upstream to the data stage) and explainability (Grad-CAM / saliency held to the reviewer bar — Adebayo sanity checks, quantitative localisation vs ground truth, attribution-not-validation framing, via check_explainability_report). Plus a by-stage skill index, multi-host README/About (Claude Code · Codex · Cursor · Copilot), copy-paste citation ergonomics, and a real-project precision fix. Additive and backward-compatible; 53 skills / 46 guidelines / 48 integrity detectors / 22 domain-probe modules. (See the CHANGELOG for v5.0–v5.14.)

v4.10 — reviewer-coverage expansion reverse-engineered from high-IF, CC-BY papers (learn-only under the reverse_engineer/ license firewall), plus a clinician-friendly update path. Additive and backward-compatible; 45 skills / 46 guidelines / 36 detectors / 15 domain-probe modules (was 12):

  • Three new reviewer domain-probe modules (/peer-review + /self-review, vendored byte-identical): Mendelian randomization (MR1–MR8 — IV assumptions, pleiotropy-robust sensitivity suite, Steiger, sample overlap, NLMR, drug-target colocalization), polygenic risk score (PG1–PG8 — ancestry portability, base/target leakage, incremental value over the clinical model, screening-vs-discrimination, calibration), and network meta-analysis (NM1–NM8 — transitivity, incoherence, SUCRA over-interpretation, CINeMA/GRADE-NMA, component-NMA additivity). Plus observational O17 (agnostic many-exposure-scan multiplicity: ExWAS/EWAS/MWAS).
  • Two reporting-guideline checklists (36 → 38): STROBE-MR and PGS-RS / PRS-RS, with study-type routing. Four new /analyze-stats analysis guides (multiplicity, MR, PRS, NMA) and a /clean-data implausible-value + cross-field validity reference.
  • Clinician-friendly update reminders — the classroom installers enable the in-app "update available" notice + one-click Desktop updater by default; the npx/manual paths print how to turn it on; the install guide recommends npx medsci-skills install --enable-update-notify.

v4.9 — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 46 guidelines, analysis-integrity detectors 32 → 36:

  • Four new gates — a duplicate-bibliography check (check_reference_duplication.py) for the hybrid [@key] + hand-typed ## References build that renders the list twice; a cross-script binning / composite-indicator consistency check (check_binning_consistency.py, BINNING_DRIFT / DERIVED_DEF_DRIFT) for a derived categorical or composite indicator defined inconsistently across analysis scripts; a float citation-order check (check_citation_order.py) for numbered Tables/Figures not first cited in ascending order per series; and an audit-dump leak gate (/sync-submission) that blocks a /check-reporting output mistakenly attached as a submission file.
  • KJR technical-check conventions + percentage-decimal style, reader-allocation-under-burden and generative-image-as-study-object reporting (/design-ai-benchmarking, /check-reporting), and a Liver International CSL with that journal's submission mechanics (/manage-refs).

v4.8 is the review-harvest batch — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 46 guidelines, analysis-integrity detectors 30 → 32:

  • Two new gatescheck_supplement_hygiene.py lints the rendered supplement / tables / caption files (not just the manuscript) for §-labels, placeholders, build markers, response-letter framing, and unresolved body↔supplement cross-references; check_null_calibration.py flags a headline negative/equivalence claim made without a minimum-detectable-effect / power / equivalence statement.
  • Four detector false-positive fixes — gates no longer fire on a recommended colorblind-safe palette, author-footnote § daggers, a correctly-hedged disclaimer, or a tier-label digit; each with a regression fixture and three newly CI-wired test suites.
  • Nine reviewer-side domain probes (SR/MA, observational, diagnostic, AI-overclaiming, survival) plus a /design-study design-stage ceiling gate for perceptual/reader-AI studies and a reusable confidence-weighted-rating→AUC monotonicity template.

v4.7 is the self-update foundation — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 46 guidelines / 30 detectors:

  • Transactional, crash-recoverable installer. Each install runs through a durable journal state machine recovered on the next run (roll back / forward-clean / fail-closed), with per-target SHA-256 inventories — your modified or third-party skills are backed up and never clobbered or auto-deleted.
  • One-click self-updater (~/.medsci-skills/updater/, install.py --check-update). Verifies the download against the github.com API digest and never extractall()s (per-entry rejection of traversal / symlink / duplicate / zip-bomb + an allowlist & per-file hash). The release pipeline injects a verified provenance.json, attests build provenance, runs on a protected release environment, and verifies each ZIP round-trips through the updater's own safe-extract before publishing.
  • Opt-in update notice (off by default): install.py --enable-update-notify shows a one-line "update available" message at Claude Code session start — no telemetry, reads nothing about your session, installs nothing. --disable-update-notify / MEDSCI_NO_UPDATE_CHECK=1 turn it off. (Honest scope: the digest/attestation detect transport tampering, not a compromised publisher account — see SECURITY.md.)

v4.6 is a maintainability, governance, and review-depth release — still 45 skills / 46 guidelines; analysis-integrity detectors 28 → 30, domain probes 11 → 12:

  • Fairness / equity / subgroup-performance probe (EQ0–EQ6) for AI/prediction/diagnostic studies that claim cross-population performance, plus two new detectors: an AI-disclosure + data/code-availability check (/sync-submission) and a structured-summary-box conformance check (/academic-aio).
  • Governance + answer-engine layer: ROADMAP.md, MAINTAINERS.md, SECURITY.md, a maintainer workflow + release checklist, an AEO/GEO docs/faq.md, a "Start here: 3 workflows" + "Validation status" section in this README, and a new maturity field (official / experimental / community) on every skill.
  • Token diet (pilot): write-paper Phase 7 integrity audits moved to a load-on-demand reference (~2,559 tokens saved per invocation). Positioning now leads with the compliance moat rather than skill count.

v4.5 deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 46 guidelines); analysis-integrity detectors 27 → 28:

  • /clean-data + /analyze-stats — reverse-coded-item / negative-alpha detector. A multi-item Likert scale with a negatively-worded item must be recoded (min+max) − x before the scale total or Cronbach's alpha is computed; left un-recoded, the item correlates negatively with the rest of the scale and alpha collapses (often negative). A negative alpha is a coding bug, not a "multidimensional construct." New stdlib-only check_reverse_coding.py returns REVERSE_CODING_LIKELY / REVERSE_CODING_SUSPECT / OK from per-item item-rest correlations + raw alpha; the Likert summary template gains a --reverse-items recode flag.
  • /peer-review + /self-review — SR/MA + DTA + prediction-model probe batch. sr_ma.md P12 risk-of-bias table row-sum ↔ traffic-light figure-matrix reconciliation and P13 included-study ↔ reference-list completeness; diagnostic_accuracy.md D7 index-test-as-enrollment-criterion circularity; clinical_prediction_model.md CP5 intended-use horizon leakage and CP6 development/CV vs held-out/external validation-nomenclature conflation. Vendored byte-identical into /self-review.
  • /sync-submission — embedded absolute-path leak scan. A word/*.xml attribute (e.g. a pandoc-embedded image's <pic:cNvPr descr="…">) carrying an absolute home-dir path (/Users/…, /home/…) is a username leak invisible to a rendered-text scan; now flagged as docx_embedded_abs_path under check_asset_anonymization.py.

v4.4 adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 46 guidelines / 27 detectors):

  • /author-strategy — trajectory-archetype classification (optional). Classifies a queried author's PubMed trajectory into abstract career archetypes (A1 infrastructure builder, A2 methodology rule-maker, A3 clinical→AI hybrid, A4 SR/MA volume engine, A5 large-consortium participation, A6 device/technique depth, + a computed composite) as an explainable, multi-label, confidence-scored heuristic — not an objective verdict. The rubric is a single canonical YAML (the narrative doc is generated from it); scores exclude unavailable signals (h-index/citation/venue-tier → [VERIFY], never fabricated); a disambiguation gate binds an approved corpus_manifest.json to the CSV (csv + PMID-set hashes) so a surname alone never classifies, and target-author attribution never borrows a co-author's ORCID/affiliation.
  • /peer-review + /self-review — Image-Synthesis / cross-modality probe (IS1–IS4) for studies that synthesize one imaging modality from another and claim the output carries the target's information, plus a reviewer-side reference-integrity spot-check.
  • /verify-refs — OpenAlex tertiary index recovers conference-proceedings / non-DOI citations (NeurIPS/ICLR/ACL) that fall through PubMed and CrossRef, the free analogue of a portal's second index.

v4.3 hardens the cross-sectional / observational cohort review surface end-to-end, much of it reverse-engineered from real CC-BY cohort papers (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 46 guidelines); analysis-integrity detectors 25 → 27:

  • Observational probes O1 → O14 (/peer-review + /self-review, vendored) — over-adjustment / analysis-unit clustering / outcome construct-validity (O7–O9), overlapping-subset gradient (O10), complex-survey design & weighting for NHANES/KNHANES (O11), data-driven threshold / "inflection-point" mining (O12), cross-sectional mediation temporal-order & sequential-ignorability (O13), and interaction scale — additive RERI/AP/S vs multiplicative (O14). Plus a new clinical-prediction-model probe module CP1–CP4 and survival S9 (panel-data / multistate variance).
  • Two new detectors (25 → 27)check_wordcount_cap.py (the revision-inflation trap: body vs journal cap) and check_paren_spans.py (em-dash→paren conversions that wrap a whole sentence). Plus a check_confounding_completeness.py upgrade (DB-code↔prose alias map, SMD-from-mean±SD, exposure-defining-covariate exemption), a check_cohort_arithmetic.py ANALYSIS_UNIT_UNDISCLOSED check, a check_scope_coherence.py cross-sectional-yield lexicon, and a verify-refs corporate/collective-author render-abort fix.
  • Analysis & submission tooling/analyze-stats gains mediation and interaction & effect-modification guides; /sync-submission gains assemble_supplement.py (S{N} index↔file integrity) and a /revise body-word-count exit gate; /render-pdf-doc gains a scan_glyph_coverage.py xelatex silent-glyph-drop scan.

v4.2 builds out the case-report capability end-to-end, grounded in real CC-BY case reports (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 46 guidelines); journal profiles 68 → 73:

  • Case-report + case-series writing/write-paper gains a CARE narrative + 150-word-abstract case-report exemplar, a case-series paper type (methods-light mini-cohort, all-cases summary table, counts-not-rates), and adverse-event/pharmacovigilance (Naranjo/WHO-UMC causality) and diagnostic-pitfall/mimic subtypes.
  • Radiology / imaging-led track — a dedicated exemplar_case_report_radiology.md (per-modality technique→findings→impression, structured-reporting lexicons BI-RADS/LI-RADS/PI-RADS/TI-RADS/Lung-RADS/O-RADS, quantitative threshold honesty, an interventional-radiology procedure/complication subtype, DICOM de-identification) plus a /make-figures annotated multimodality imaging-panel exemplar.
  • Case-report reviewer probe/peer-review + /self-review ship a vendored case-report domain probe CR1–CR9 (novelty/consent/n=1 causality, case-series design, adverse-event causality, imaging-led discipline).
  • Where to submit — compact /find-journal profiles for Journal of Medical Case Reports, Cureus, Radiology Case Reports, BMJ Case Reports, and BJR Cas