Medical Research Skills for Claude Code

Single entry point for the full bundle. Classifies your request and routes to the right skill — or chains multiple skills end-to-end via Full Pipeline Mode.

• ✓Automatic intent classification
• ✓End-to-end pipeline: skills chain automatically
• ✓Project context detection

PubMed + Semantic Scholar + bioRxiv search with anti-hallucination citation verification. Token-efficient error handling.

• ✓Every reference verified via API
• ✓BibTeX export with verified / verified_by / verified_on fields
• ✓No fabricated citations

Pre-submission reference audit for .md / .docx / .bib / .tsv inputs. Extracts references, verifies DOI/PMID via CrossRef + PubMed, and writes qc/reference_audit.json as the sole source of truth. Blocks fabricated references before submission.

• ✓DOI + PMID verification via CrossRef & PubMed
• ✓Writes verified_references.tsv, library.bib, reference_audit.json
• ✓PostToolUse hook auto-runs on manuscript saves (auto / warn / enforce modes)

Batch open-access PDF downloader. Unpaywall → PMC → OpenAlex → CrossRef pipeline. OA-only — no paywall bypass.

• ✓DOI list or TSV input
• ✓PDF validation built-in
• ✓Manual-needed list for paywalled papers

Manuscript compliance audit against 33 reporting guidelines and risk-of-bias tools with item-by-item assessment and section boundary checks.

• ✓STROBE, STARD, STARD-AI, PRISMA, CONSORT, TRIPOD+AI, CARE, MI-CLEAR-LLM
• ✓QUADAS-2, RoB 2, ROBINS-I, PROBAST, NOS
• ✓Results/Discussion boundary check

Identifies analysis unit, cohort logic, data leakage risks, and validation strategy.

• ✓Leakage risk detection
• ✓Comparator design review
• ✓Reporting guideline matching

Reproducible Python/R code for 13 analysis types including regression, propensity score, and repeated measures. Calibration mandatory for prediction models.

• ✓Regression (logistic/linear), propensity score (PSM/IPTW), repeated measures (GEE/mixed)
• ✓DTA, survival, demographics, agreement
• ✓Publication-ready tables with journal-specific formatting

Journal-spec figures and visual abstracts: ROC curves, forest plots, flow diagrams, Kaplan-Meier, and more.

• ✓300 DPI, colorblind-safe
• ✓PRISMA / CONSORT / STARD flows
• ✓Visual/graphical abstracts (python-pptx template)

Structures significance, innovation, approach, milestones, and consortium roles.

• ✓NIH / NRF format support
• ✓Specific aims page
• ✓Budget justification

Classifies new research projects, summarizes state, and recommends next steps.

• ✓Project type classification
• ✓Missing input detection
• ✓Lightweight scaffolding

Academic presentation prep: paper analysis, speaker scripts, slide note injection, Q&A.

• ✓Audience-adapted scripts
• ✓PPTX note injection utility
• ✓Multi-perspective Q&A prep

Convert personal Claude Code skills into distributable, open-source-ready packages.

• ✓Automated PII audit
• ✓License compatibility check
• ✓Generalization pipeline

Full 8-phase systematic review and meta-analysis pipeline. DTA (bivariate/HSROC) and intervention MA with PRISMA-DTA compliance.

• ✓Protocol to manuscript pipeline
• ✓Bivariate & HSROC models
• ✓PRISMA-DTA compliant

Full 8-phase IMRAD pipeline from outline to submission-ready manuscript with built-in critic-fixer loops and section boundary enforcement.

• ✓Anti-interpretation guardrails in Results
• ✓Interactive Discussion with anchor papers
• ✓AI writing pattern detection

Pre-submission check across 10 categories with research-type branching (AI, observational, educational, meta-analysis, case report, surgical).

• ✓Major / Minor severity classification
• ✓Calibration mandatory for prediction models
• ✓R0 numbering for /revise pipeline

Parses reviewer decision letters, classifies comments as MAJOR/MINOR/REBUTTAL, and generates point-by-point responses.

• ✓Structured response templates
• ✓Change log with page/line refs
• ✓Cover letter generation

Scaffold research projects, track writing progress, generate submission checklists and backwards timelines.

• ✓Project scaffolding with --zotero-collection auto-create (pyzotero)
• ✓Phase progress tracking
• ✓Pre-submission checklist

SSOT-to-submission drift audit and journal package helper. Treats submission/{journal}/ as derived output, records source hashes in .journal_meta.json, and blocks freezing drifted packages.

• ✓SHA-256 source-hash drift detection
• ✓Per-journal package freeze / unfreeze workflow
• ✓Blocks submission when SSOT has diverged

Interactive sample size calculator with decision-tree guided test selection. Covers 11 designs including Cox regression EPV.

• ✓DTA, t-test, ANOVA, chi-square, McNemar, survival
• ✓Logistic regression & Cox EPV (Peduzzi rule)
• ✓IRB-ready justification text

Standardize, validate, and transform raw research datasets. Handles missing data, outlier detection, and variable recoding.

• ✓Missing data summary & imputation
• ✓Outlier detection (IQR, Z-score)
• ✓Codebook generation

Match your manuscript to target journals by scope, impact factor, turnaround time, and open-access policy.

• ✓Scope & audience matching
• ✓Impact factor / CiteScore lookup
• ✓OA fee & turnaround estimates

Generate SPIRIT-compliant study protocols and PROSPERO registration drafts for systematic reviews.

• ✓SPIRIT checklist integration
• ✓PROSPERO registration draft
• ✓Ethics submission boilerplate

Add new journal profiles to the database. Extracts metadata from author guidelines and generates dual profiles (write-paper + find-journal) with quality gates.

• ✓Author guideline extraction
• ✓Dual profile generation
• ✓Batch mode for multiple journals

De-identify clinical research data before LLM-assisted analysis. Standalone Python CLI with 10 country locale packs. No LLM involved.

• ✓PHI detection via regex + heuristics
• ✓Interactive terminal review
• ✓Date shifting & pseudonymization

Research gap finder for longitudinal cohort databases. 6-phase pipeline (cohort intake → PI profiling → intersection matrix → literature saturation scan → 6-Pattern scoring → feasibility gate) that outputs ranked topic proposals with comparison tables and one-pagers.

• ✓Works with any cohort: NHIS, UK Biobank, institutional EMR, health checkup registries
• ✓6-Pattern gap scoring with feasibility gate
• ✓Ranked proposals with one-pager output

Replicate an existing cohort study on a different database. Extracts methodology from a source paper, maps variables via harmonization table, generates analysis code, and produces a replication difference report.

• ✓5-phase workflow: source analysis → variable mapping → code generation → difference report → verification
• ✓Built-in KNHANES/NHANES harmonization table
• ✓Validated on Joo 2026 cross-national replication

End-to-end cross-national comparison study using parallel survey data. Variable harmonization, parallel weighted analysis (no data pooling), and country-stratified comparison tables.

• ✓KNHANES + NHANES + CHNS variable coding references
• ✓Country-specific survey design with no data pooling
• ✓Supports 2-country and 3-country designs

Generate N analysis scripts from one validated template × multiple exposure/outcome combinations. The "80-person team" pattern: same method, swap variables only.

• ✓Self-adjustment prevention & EPV checks
• ✓Bonferroni correction & summary heatmaps
• ✓Validated: 18 combos on KNHANES, 45 combos across 3 countries

Fill Korean IRB and institutional Word form templates (.doc/.docx) while preserving original layout, cell structure, and formatting. Extracts content from your protocol draft and maps it to labeled form cells.

• ✓Preserves original form structure — no layout breakage
• ✓Cell label matching for Korean IRB forms
• ✓LibreOffice conversion with original backup

Batch-fill ICMJE Conflict of Interest Disclosure forms (.docx) for co-authors from a pre-filled seed document. Replaces date, author name, and manuscript title while keeping the 13-item disclosure block and checkbox states intact.

• ✓Ships with a PII-free synthetic seed (safe to redistribute)
• ✓Literal XML replacement inside Word Content Controls (SDTs)
• ✓Post-run verification: 14 ☒, 13 "None", zero placeholder leakage

Detect and remove AI writing patterns from academic manuscripts. Scans for 18 common patterns — significance inflation, AI vocabulary, copula avoidance — and rewrites flagged passages while preserving technical accuracy.

• ✓18-pattern detection with per-instance flagging
• ✓Density target: <2.0 AI instances per 1,000 words
• ✓Rewrites preserve all numbers, p-values, and clinical terms

PubMed author profile analysis. Fetches publication history via E-utilities, classifies study types (GBD, SR/MA, NHIS, AI/ML, etc.), generates 7 visualizations, and produces a strategy report with replication opportunities.

• ✓E-utilities batch fetch with deduplication
• ✓Study type classifier: GBD, SR/MA, NHIS, AI/ML, cross-national, case series
• ✓Replication opportunity scoring with co-author gap analysis

Structured peer review drafting for medical imaging journals. Systematic manuscript analysis, journal-specific formatting (RYAI, INSI, EURE, AJR, KJR), conciseness targets (500–800 words), and pre-submission QC checklist.

• ✓Major / Minor / Reject recommendation with rationale
• ✓Journal-specific format presets for 5 radiology journals
• ✓Pre-submission QC: word count, tone, ethical red flags

Meta-analysis topic discovery and feasibility assessment. Two modes: Professor-first (profile → pillar analysis → MA gaps) or Topic-first (question → landscape scan → co-author matching). Multi-source validation with realistic k estimation.

• ✓Professor-first and Topic-first dual modes
• ✓Multi-source validation: PubMed, PROSPERO, bioRxiv
• ✓Realistic k estimation with 15–30% registration discount

Sync research references from .bib files to Zotero library + Obsidian literature notes. Concept extraction from 10+ accumulated notes with cross-cutting theme discovery. Works after /search-lit or standalone.

• ✓Zotero import via Better BibTeX key matching
• ✓Obsidian literature note generation with wikilinks
• ✓Cross-cutting concept extraction from 10+ notes

Visibility checklist for medical AI papers against AI search engines (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace) and RAG literature tools. Integrates TRIPOD+AI, CLAIM, STARD-AI, TRIPOD-LLM, DECIDE-AI with generative-engine-optimization (GEO) principles.

• ✓Covers title, abstract, Key Points, Plain-Language Summary, preprints, README, CITATION.cff, Zenodo, Hugging Face cards
• ✓Defends against LLM citation fabrication (Agarwal 2025)
• ✓Visible PASS / PARTIAL / FAIL checklist — never applies silent edits

Citekey ↔ .bib validation, journal-CSL pandoc rendering, manuscript ↔ rendered DOCX cross-reference QC, [N] ↔ [@key] marker conversion, and native Zotero CWYW field-code injection for co-author Word workflows. Sole writer of manuscript_final.docx and qc/xref_audit.json. Hybrid 3-phase strategy (pandoc draft → CWYW transition → Zotero CWYW for circulation/revision/submission).

• ✓check_citation_keys.py + check_xref.py --strict as the submission gate
• ✓Bundled journal CSLs: ER, Radiology, AJR, CVIR, KJR, Vancouver — cascade-rejection re-render in seconds
• ✓Native CSL-JSON CWYW injection (handles webpage / report / non-journal item types correctly)

Render non-bibliography academic markdown (proposal, briefing handout, anchor doc, IRB cover, reference table) to publication-quality PDF via pandoc + xelatex. Boundary opposite of manage-refs — non-bib, layout-focused.

• ✓CJK font fallback: Apple SD Gothic Neo (macOS), Noto Sans CJK KR (Linux)
• ✓Content-proportional pipe-table column widths — first column shrinks to fit, data columns share the remainder
• ✓Frontmatter redact_internal flag for circulation PDFs (no version numbers / changelog / PI attribution leakage)

Literature-grounded variable operationalization for observational research. Turns a data dictionary plus research question into a citation-backed table of exposure / outcome / covariate definitions, cutoffs, and DB-variable mappings. Tier 0 dictionary-first rule prevents ad-hoc phenotype definitions that invite reviewer rejection.

• ✓Dictionary-first Tier 0 enforcement (verbatim citation of codebook entries)
• ✓Bridges /search-lit output into /write-protocol Methods
• ✓Per-variable citation provenance (source / row / verbatim mapping)