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Updated today

by Aperivue

medsci-skills

Agent Skills for medical research — literature search, reporting-guideline & citation checks, statistics, publication figures, submission. Works with Claude Code, Codex, Cursor & GitHub Copilot. Built by a physician-researcher, tested on real publications. MIT.

  • Active — Updated in the last 14 days
  • Multi-agent — Targets three or more agents
Works with
  • Claude
  • Codex
  • Cursor
  • Copilot
View on GitHub (opens in a new tab)

340 GitHub stars (340)

+24 in 20 days

Stars gained per day · daily snapshots since Sep 26
Stars gained per day, Sep 26 to Oct 16: +24 in total; the busiest day was Sep 30 with +3 stars.Sep 27: 0 starsSep 28: +2 starsSep 29: +1 starsSep 30: +3 starsOct 1: 0 starsOct 2: 0 starsOct 3: +1 starsOct 4: +2 starsOct 5: +1 starsOct 6: +3 starsOct 7: 0 starsOct 8: 0 starsOct 9: +2 starsOct 10: +2 starsOct 11: 0 starsOct 12: +1 starsOct 13: +2 starsOct 14: +1 starsOct 15: +3 starsOct 16: 0 stars
Stars gained between daily snapshots
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Sep 270
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Oct 160
  • 30 skills (30 skills found in its SKILL.md files)
  • 78 forks (78 forks)
  • Today last update (Last updated today)

Install

Skills CLI

npx skills add Aperivue/medsci-skills

Asks which skills and agents to install. Just one: npx skills add Aperivue/medsci-skills --skill academic-aio — add -g for every project.

Claude Code

git clone https://github.com/Aperivue/medsci-skillscp -r "medsci-skills/skills/academic-aio" ~/.claude/skills/

Copies the academic-aio skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.

Plugin

/plugin marketplace add Aperivue/medsci-skills

Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.

Skills can run code on your machine — read the SKILL.md first.

What it does

In the author's own words, from each skill's SKILL.md — showing the first 30 of 60 files.

  • academic-aio

    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 journals (Lancet Digital Health, Radiology, Radiology-AI, npj Digital Medicine, N…

    skills/academic-aio/SKILL.md on GitHub (opens in a new tab)

  • add-journal

    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.

    skills/add-journal/SKILL.md on GitHub (opens in a new tab)

  • analyze-stats

    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.

    skills/analyze-stats/SKILL.md on GitHub (opens in a new tab)

  • architecture-zoo

    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 medical-imaging use, a reference implementation, the typical validation setup, and th…

    skills/architecture-zoo/SKILL.md on GitHub (opens in a new tab)

  • author-strategy

    PubMed author profile analysis. Author name → PubMed fetch → study-type classification → visualization → strategy report → optional trajectory-archetype classification.

    skills/author-strategy/SKILL.md on GitHub (opens in a new tab)

  • batch-cohort

    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.

    skills/batch-cohort/SKILL.md on GitHub (opens in a new tab)

  • calc-sample-size

    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 non-inferiority/equivalence designs.

    skills/calc-sample-size/SKILL.md on GitHub (opens in a new tab)

  • check-reporting

    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, TRIPOD-LLM, PGS-RS, ARRIVE, PRISMA, PRISMA 2020 for Abstracts, PRISMA-DTA, PRISM…

    skills/check-reporting/SKILL.md on GitHub (opens in a new tab)

  • clean-data

    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 confirmation.

    skills/clean-data/SKILL.md on GitHub (opens in a new tab)

  • contribute

    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 every line, and sends nothing until you confirm. Also files feedback: a detecto…

    skills/contribute/SKILL.md on GitHub (opens in a new tab)

  • cross-national

    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.

    skills/cross-national/SKILL.md on GitHub (opens in a new tab)

  • define-variables

    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 output into /write-protocol Methods.

    skills/define-variables/SKILL.md on GitHub (opens in a new tab)

  • deidentify

    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.

    skills/deidentify/SKILL.md on GitHub (opens in a new tab)

  • design-ai-benchmarking

    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, LLM-as-judge versus human-as-judge adjudication, construct-independence guards, and…

    skills/design-ai-benchmarking/SKILL.md on GitHub (opens in a new tab)

  • design-study

    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.

    skills/design-study/SKILL.md on GitHub (opens in a new tab)

  • explainability

    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 against ground truth (IoU / pointing game / Dice) instead of eyeballed examples, a…

    skills/explainability/SKILL.md on GitHub (opens in a new tab)

  • fill-icmje-coi

    Batch-generate per-author ICMJE Conflict of Interest Disclosure Forms (`coi_disclosure.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 replaced. Designed for the common case of hospital-based observational research wh…

    skills/fill-icmje-coi/SKILL.md on GitHub (opens in a new tab)

  • fill-protocol

    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 renders it into the institutional template. Korean-aware (CJK eastAsia font enforce…

    skills/fill-protocol/SKILL.md on GitHub (opens in a new tab)

  • find-cohort-gap

    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.

    skills/find-cohort-gap/SKILL.md on GitHub (opens in a new tab)

  • find-journal

    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. Impact-factor and APC figures in a profile are point-in-time and may be stale — verify c…

    skills/find-journal/SKILL.md on GitHub (opens in a new tab)

  • fulltext-retrieval

    Batch download open-access PDFs by DOI using legitimate OA APIs (Unpaywall, PMC, OpenAlex, Crossref). Optional PDF→Markdown conversion for token-efficient LLM analysis.

    skills/fulltext-retrieval/SKILL.md on GitHub (opens in a new tab)

  • generate-codebook

    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 DICTIONARY] rather than guessing them, feeding /define-variables and the dictionary-…

    skills/generate-codebook/SKILL.md on GitHub (opens in a new tab)

  • grant-builder

    Grant and challenge proposal support for radiology and medical AI projects. Structures significance, innovation, approach, milestones, and consortium roles while keeping claims evidence-based and executable.

    skills/grant-builder/SKILL.md on GitHub (opens in a new tab)

  • humanize

    Detect and remove AI writing patterns from academic manuscripts and response-to-reviewers letters. Scans for 27 common AI-generated text patterns and rewrites flagged passages to sound naturally human-written while preserving technical accuracy, bounding how much of the text a rewrite is allowed to touch.

    skills/humanize/SKILL.md on GitHub (opens in a new tab)

  • intake-project

    Intake and normalize a new radiology research project. Classifies project type, summarizes current state, identifies missing inputs, recommends next steps, and scaffolds lightweight project memory files.

    skills/intake-project/SKILL.md on GitHub (opens in a new tab)

  • lit-sync

    Sync research references from .bib files to Zotero library + Obsidian literature notes. Extract cross-cutting concept notes when enough literature accumulates. Works after /search-lit or standalone.

    skills/lit-sync/SKILL.md on GitHub (opens in a new tab)

  • ma-scout

    Meta-analysis topic discovery and feasibility assessment. Professor-first (profile → gap) or Topic-first (question → gap → co-author). Pre-protocol phase from idea to ranked topic list.

    skills/ma-scout/SKILL.md on GitHub (opens in a new tab)

  • make-figures

    Generate publication-ready figures and visual abstracts for medical research papers. Supports ROC curves, forest plots, CONSORT/STARD/PRISMA flow diagrams, calibration plots, Kaplan-Meier curves, Bland-Altman plots, confusion matrices, pipeline diagrams, and journal-specific visual/graphical abstracts (python-pptx template-based).

    skills/make-figures/SKILL.md on GitHub (opens in a new tab)

  • manage-project

    Research project management for medical manuscripts. Scaffold project structure, track writing progress across phases, maintain project memory files, generate submission checklists and backwards timelines. Commands: init, status, sync-memory, checklist, timeline.

    skills/manage-project/SKILL.md on GitHub (opens in a new tab)

  • manage-refs

    Cross-cutting reference manager for medical manuscripts. Single entry point for citation-key validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, marker conversion (``[N]`` ↔ ``[@key]``), and native Zotero CWYW field-code injection. Replaces the inline reference-handling that previously lived in ``/write-paper`` Phase 7.6 and is reused by ``/revise``, ``/peer-review``,…

    skills/manage-refs/SKILL.md on GitHub (opens in a new tab)

Review before you install

A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.