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Updated 3d ago

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)

365 GitHub stars (365)

+36 in 30 days

Stars gained per day · daily snapshots since Sep 26
Stars gained per day, Sep 26 to Nov 5: +49 in total; the busiest day was Oct 17 with +4 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 starsOct 17: +4 starsOct 18: 0 starsOct 19: 0 starsOct 20: +2 starsOct 21: +1 starsOct 22: +1 starsOct 23: +1 starsOct 24: 0 starsOct 25: 0 starsOct 26: 0 starsOct 27: +3 starsOct 28: 0 starsOct 29: +1 starsOct 30: +3 starsOct 31: +1 starsNov 1: +2 starsNov 2: +3 starsNov 3: 0 starsNov 4: +2 starsNov 5: +1 stars
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  • 30 skills (30 skills found in its SKILL.md files)
  • 85 forks (85 forks)
  • 3d ago last update (Last updated 3d ago)

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 63 files.

  • academic-aio

    Use when a medical AI paper should be found and cited by AI search engines and RAG tools. Optimizes the title, abstract, summary box (Key Points, Research in Context), keywords, preprint, GitHub README/CITATION.cff and Hugging Face card, returning a visible pass/fail checklist.

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

  • add-journal

    Use when a target journal has no profile yet. Reads the journal's author guidelines and writes a detailed /write-paper profile plus a compact /find-journal profile, public or user-local private, in the canonical format with quality gates.

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

  • analyze-stats

    Use when data needs statistical analysis. Runs reproducible Python/R code for Table 1, diagnostic accuracy, agreement, regression, survival, propensity score, survey-weighted and repeated-measures models, with publication tables. Sample size is /calc-sample-size; pooling studies is /meta-analysis.

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

  • architecture-zoo

    Renamed to /model-selection in v6 (removed in v7).

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

  • author-strategy

    Use when analyzing a researcher's publication record from PubMed. Fetches an author's papers, classifies study types and author position, charts the patterns and writes a strategy report, with an optional trajectory-archetype classification. Works from PubMed metadata only.

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

  • batch-cohort

    Use when one validated cohort analysis must be repeated across many exposure/outcome pairs. Generates one R/Python script per combination from a single methodology template, changing only the variables, and aggregates the results into a summary matrix.

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

  • calc-sample-size

    Use when planning how many patients or cases a study needs before data collection (power analysis, IRB justification). Walks a decision tree to the right test and returns reproducible R/Python code and IRB-ready justification text. Analyzing collected data is /analyze-stats.

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

  • check-reporting

    Use when auditing a manuscript item by item against a reporting guideline or risk-of-bias tool. Covers 49 reporting guidelines and risk-of-bias tools (STROBE, CONSORT, STARD, TRIPOD+AI, PRISMA, QUADAS and more), marking each item PRESENT, PARTIAL or MISSING. Not a reviewer critique (/self-review).

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

  • clean-data

    Use when a clinical CSV/Excel dataset needs profiling and cleaning before analysis (missing values, outliers, duplicates, type mismatches). Profiles, flags and generates cleaning code in three stages, each gated on the researcher's approval. Never auto-cleans.

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

  • contribute

    Use when sending local changes back to the project (an added journal profile, a fixed checklist item, an adapted skill) or reporting a false positive or bug. Finds what changed, scans it for patient data, shows every line and sends nothing until you confirm.

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

  • cross-national

    Use when comparing an exposure-outcome association across countries with parallel national surveys (KNHANES, NHANES, CHNS). Harmonizes variables, runs parallel weighted analyses and builds comparison tables for 2-country (KR+US) or 3-country (KR+US+CN) designs.

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

  • define-variables

    Use when exposure, outcome, covariate or eligibility definitions and cutoffs need a citable basis before the protocol. Reads the data dictionary first, then maps each variable to a guideline or published definition and the database columns in a citation-backed table.

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

  • deidentify

    Use when clinical data may contain PHI and must be de-identified before any LLM-assisted analysis. A local Python script (no network or AI calls) detects identifiers with regex and heuristics in 12 country locale packs, with interactive terminal review.

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

  • design-ai-benchmarking

    Use when designing a study that benchmarks AI systems against a human-expert panel, before data collection. Plans the arms, decoupled rubrics with anchors, planted calibration probes, reviewer panel, inter-rater reliability targets and LLM-as-judge versus human adjudication.

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

  • design-study

    Use when checking a radiology or medical AI study design before drafting or submission. Reviews the analysis unit, cohort logic, leakage risks, comparator, validation strategy and reporting-guideline fit. AI-vs-expert benchmarks are /design-ai-benchmarking.

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

  • explainability

    Renamed to /model-assessment in v6 (removed in v7).

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

  • fill-icmje-coi

    Use when each author needs an ICMJE Conflict of Interest disclosure form (coi_disclosure.docx) for submission. Clones a pre-filled synthetic seed with every item marked None and replaces only date, name and manuscript title, so most authors just confirm or amend.

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

  • fill-protocol

    Use when an institutional Word form (.doc/.docx IRB protocol, ethics application, grant template) must be filled without breaking its styles, tables, fonts or page layout. Renders content drafted by /write-protocol into the template; CJK-aware.

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

  • find-cohort-gap

    Use when looking for research topics a longitudinal cohort database can answer (NHIS, UK Biobank, an institutional EMR or registry). Profiles the cohort, matches PI expertise, scans literature saturation and returns ranked topic proposals with gap evidence.

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

  • find-journal

    Use when choosing where to submit a manuscript. Matches the abstract against curated journal profiles and returns ranked picks with scope fit, AI-disclosure policy, an acceptance-readiness pre-flight and a reject-fallback cascade. Impact and APC figures may be stale.

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

  • fulltext-retrieval

    Use when you need full-text PDFs for a list of DOIs, such as a meta-analysis screening set. Batch-downloads open-access copies via Unpaywall, PMC, OpenAlex and Crossref, lists paywalled papers for manual access, and can convert PDFs to Markdown.

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

  • generate-codebook

    Use when a tabular dataset (CSV, Excel, Parquet, Stata, SAS) needs a data dictionary. Profiles every variable (type, levels, range, missingness) into codebook.md and codebook.json and flags coded values of unknown meaning as [NEEDS DICTIONARY] instead of guessing.

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

  • grant-builder

    Use when drafting a grant or challenge proposal for a radiology or medical AI project, including a Korean government industry-academia plan. Structures significance, innovation, approach, aims, milestones and consortium roles, keeping claims evidence-based and executable.

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

  • humanize

    Use when a manuscript or response-to-reviewers letter reads as AI-written. Scans for 27 AI writing patterns and rewrites flagged passages, preserving technical accuracy and bounding how much text changes. Not general copy-editing; that is /polish-language.

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

  • imaging-data

    Use when preparing a medical-imaging dataset (DICOM/NIfTI) for modelling. Profiles spacing, orientation, intensity, label integrity, foreground fraction and target volume, gates them against the plan, then plans and audits preprocessing and augmentation for leakage.

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

  • intake-project

    Use when starting or inheriting a radiology research project and need to know what it is. Classifies the project type, summarizes its current state, lists 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

    Use when references in a .bib file (often from /search-lit) should land in Zotero and Obsidian. Syncs them to the Zotero library, writes Obsidian literature notes and extracts cross-cutting concept notes once enough accumulate. A folder of PDFs is /obsidian-paper-vault.

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

  • ma-scout

    Use when looking for a meta-analysis topic before any protocol exists. Starts from a professor's publication profile or from a clinical question, finds gaps, assesses feasibility and returns a ranked topic list. Running the review itself is /meta-analysis.

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

  • make-figures

    Use when a paper needs publication-ready figures or a visual abstract. Makes ROC, forest, calibration, Kaplan-Meier and Bland-Altman plots, CONSORT/STARD/PRISMA flow diagrams, confusion matrices, pipeline diagrams and journal visual abstracts, checking the journal's AI-image policy first.

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

  • manage-project

    Use when managing a manuscript project over time. Scaffolds the project structure, tracks writing progress across phases, maintains project memory files, and generates submission checklists and backwards timelines (commands init, status, sync-memory, checklist, timeline).

    skills/manage-project/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.