Use when drafting a medical research manuscript or any IMRAD section. Runs an 8-phase pipeline from outline to submission-ready draft for original articles, AI validation studies, case reports, meta-analyses, technical notes and more. Checking a draft is /self-review.
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Use when writing a literature review article (narrative, scoping PRISMA-ScR or systematic). Scaffolds a 7-part skeleton with a scope and non-overlap statement, summary-table stubs and reporting-guideline wiring, without inventing citations. Original research is /write-paper.
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Use when building, auditing or freezing a journal submission package from the canonical manuscript. Detects drift between the source and the per-journal submission copy, builds byte-preserving packages with manifests, and records current, stale or frozen status.
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Renamed to /model-assessment in v6 (removed in v7).
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Use when finding papers or building a reference list. Searches PubMed, Semantic Scholar and bioRxiv/medRxiv, includes only references verified through an API, and generates BibTeX. Auditing an existing reference list is /verify-refs.
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Use when applying a published cohort study's methodology to a different database. Extracts the design from the source paper, maps variables to the target database with a harmonization table, generates the analysis code and reports every forced deviation.
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Use when a manuscript comes back with reviewer or editor comments. Numbers every comment, classifies it MAJOR/MINOR/REBUTTAL, drafts a point-by-point response with tracked manuscript changes, routes new analyses to /analyze-stats and writes the cover letter.
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Use when a skill fails for a missing tool or the environment needs checking. Diagnoses Python, R, Node, Claude Code, Git, Zotero and configured MCP servers and prints a pass/fail table with links to the setup docs. Read-only; installs nothing.
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Use when drafting an IRB or ethics research protocol. Writes Background, Study Design, Sample Size and Statistical Plan in full prose and leaves institution-specific sections as TODO skeletons. Filling an institutional Word form is /fill-protocol.
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Use when checking whether a manuscript's references are real. Audits each citation against PubMed and CrossRef, flags fabricated or mismatched entries and writes qc/reference_audit.json. Audit-only; never edits references or refs.bib. Citation-key checks are /manage-refs.
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Use when you must prove an analysis ran on the intended data or lock a dataset version. Builds a deterministic content-hash manifest (file SHA-256, schema, per-column value hashes), verifies later copies against it for drift, and diffs two manifests.
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Use when checking your own manuscript before submission from a reviewer's perspective. Returns anticipated Major/Minor comments with fixes, including numerical, citation and leakage checks, with an optional multi-reviewer panel. Someone else's paper is /peer-review.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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