Plugin Claude Code
Physician-built Claude Code skills for clinical manuscript preparation, with deterministic integrity gates — reporting-guideline and risk-of-bias compliance, reference/citation verification, and numerical-consistency checks — plus literature search, study design, statistics, publication-ready figures, IMRAD drafting…
Instructions file
Instructions for Aperivue/medsci-skills, covering working in this repository and everything else.
Skill Claude CodeCodex
Medical AI paper optimization for AI search engines (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace) and RAG-based literature tools. Applies when drafting or reviewing titles, abstracts, structured summary boxes (Key Points / Research in Context / Plain-Language Summary), manuscripts for high-impact medical AI…
Skill Claude CodeCodex
Add a new journal to the MedSci Skills profile database. Extracts metadata from author guidelines, generates write-paper (detailed) and find-journal (compact) profiles in canonical format with quality gates.
Skill Claude CodeCodex
Statistical analysis for medical research papers. Generates reproducible Python/R code with publication-ready tables and figures. Supports diagnostic accuracy, inter-rater agreement, meta-analysis, survival analysis, survey data, group comparisons, regression, propensity score, and repeated measures.
Skill Claude CodeCodex
Choose a model architecture for a medical-imaging research question before scaffolding. Maps the task (classification, segmentation, detection, transfer), modality and dimensionality, labelled-data scale, and class imbalance to a shortlist of architectures, each grounded in its source paper with a when-to-use, a…
Skill Claude CodeCodex
PubMed author profile analysis. Author name → PubMed fetch → study-type classification → visualization → strategy report → optional trajectory-archetype classification.
Skill Claude CodeCodex
Generate N analysis scripts from a single methodology template × multiple exposure/outcome combinations. The "80-person team" pattern — same validated method, swap variables only. Produces batch R/Python code + summary matrix.
Skill Claude CodeCodex
Interactive sample size calculator for medical research. Decision-tree guided test selection, reproducible R/Python code, effect size interpretation, and IRB-ready justification text. Supports diagnostic accuracy, agreement, proportions, continuous outcomes, survival, ANOVA, logistic regression, and…
Skill Claude CodeCodex
Check manuscript compliance with medical research reporting guidelines. Supports 49 guidelines including STROBE, STROBE-MR, RECORD, REMARK (prognostic tumor-marker studies), TARGET (target trial emulation), GATHER (burden-of-disease / health-estimate modeling), CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD+AI…
Skill Claude CodeCodex
Interactive data profiling and cleaning assistant for medical research. Three-stage workflow (profile, flag, code-generate) with user approval gates at each step. Handles missing values, outliers, duplicates, and type mismatches in CSV/Excel clinical data. Does NOT auto-clean — all decisions require researcher…
Skill Claude CodeCodex
Offer your local changes back to the project — a journal profile you added, a checklist item you fixed, a skill you adapted to your department — as a pull request or an issue, without ever typing a git command. Detects what you changed against the installed version, scans it for patient data and identifiers, shows you…
Skill Claude CodeCodex
End-to-end cross-national comparison study using KNHANES + NHANES + CHNS (or other parallel surveys). Variable harmonization, parallel weighted analysis, and comparison tables. Supports 2-country (KR+US) and 3-country (KR+US+CN) designs.
Skill Claude CodeCodex
Literature-grounded variable operationalization for observational research. Turns a data dictionary + research question into a citation-backed table of exposure/outcome/covariate definitions, cutoffs, and DB variable mappings. Prevents ad-hoc phenotype definitions that invite reviewer rejection. Bridges /search-lit…
Skill Claude CodeCodex
De-identify clinical research data before LLM-assisted analysis. Standalone Python CLI detects PHI via regex + heuristics with 10 country locale packs (kr, us, jp, cn, de, uk, fr, ca, au, in). Interactive terminal review. No LLM touches raw data — the script runs locally without any network or AI calls.
Skill Claude CodeCodex
Design and validity review for studies that benchmark one or more AI systems against a human-expert panel as the reference. Covers the evaluation question and arm definition, decoupled multi-dimensional rubrics with anchors, planted calibration probes, reviewer-panel construction, inter-rater reliability targets…
Skill Claude CodeCodex
Study design and validity review for radiology and medical AI research. Identifies analysis unit, cohort logic, leakage risks, comparator design, validation strategy, and reporting guideline fit before drafting or submission.
Skill Claude CodeCodex
Produce or audit the interpretability/explainability analysis of a medical-imaging model — Grad-CAM / Grad-CAM++ / attention-rollout / saliency / integrated-gradients — so it clears the rigor bar a reviewer expects: mandatory Adebayo sanity checks (model- and data-randomisation), a quantitative localisation metric…
Skill Claude CodeCodex
Batch-generate per-author ICMJE Conflict of Interest Disclosure Forms (coidisclosure.docx) for manuscript submission. Pre-fills all 13 disclosure items as "☒ None" + final certification ☒ using a synthetic seed template shipped with the skill, then clones the seed per author with Date, Name, and Manuscript Title…
Skill Claude CodeCodex
Fill institutional Word form templates (.doc/.docx) for IRB protocols, ethics applications, grant proposals, and other structured research documents while preserving the original styles, table layouts, fonts, and page geometry. Pairs with write-protocol — write-protocol drafts the scientific content, fill-protocol…
Skill Claude CodeCodex
Research gap finder for longitudinal cohort databases. Profiles cohort strengths, matches PI expertise, scans literature saturation, and outputs ranked topic proposals with gap evidence. Works with any cohort: NHIS, UK Biobank, institutional EMR, health checkup registries, or disease-specific registries.
Skill Claude CodeCodex
Journal recommendation engine for medical manuscripts. 2-pass matching against a curated public profile library plus any user-local private profiles, enriched with detailed write-paper profiles for top-5 output. Returns ranked recommendations with scope fit rationale, AI disclosure policy, and homepage links.…
Skill Claude CodeCodex
Batch download open-access PDFs by DOI using legitimate OA APIs (Unpaywall, PMC, OpenAlex, Crossref). Optional PDF→Markdown conversion for token-efficient LLM analysis.
Skill Claude CodeCodex
Generate a citable data dictionary / codebook from a tabular dataset (CSV/TSV/Excel/Parquet/Stata/SAS). Profiles every variable — role, type, units placeholder, level frequencies, range/quantiles, missingness — and emits codebook.md + codebook.json. Flags coded variables whose level meanings are unknown as [NEEDS…