Aperivue/medsci-skills

peer-review

Peer review assistant for medical journals. Generates structured review drafts with journal-specific formatting. Constructive developmental tone with systematic manuscript analysis.

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.…

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…

meta-analysis

Systematic review and meta-analysis pipeline for medical research. Covers protocol registration (PROSPERO), search strategy, screening, data extraction, risk of bias assessment (QUADAS-2/ROBINS-I), statistical synthesis (bivariate/HSROC for DTA,…

publish-skill

Convert a personal agent skill into a distributable, open-source-ready skill. Runs PII audit, generalization, license compatibility check, cross-platform adapter review, and packaging workflow.

self-review

Pre-submission self-review for the user's own manuscripts, applying a reviewer perspective. Systematic check across 10 categories with research-type branching. Outputs Anticipated Major/Minor Comments with severity framing and optional R0 numbering for…

sync-submission

Audit SSOT-to-submission drift and create journal submission manifests from canonical manuscript artifacts.

write-paper

Full-pipeline medical/scientific paper writing. 8-phase IMRAD workflow from outline to submission-ready manuscript. Supports original articles, case reports, case series, meta-analyses, AI validation studies, animal studies, and technical notes. Do NOT…

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…

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…

search-lit

Literature search and citation management for medical research. Searches PubMed, Semantic Scholar, and bioRxiv/medRxiv with verified citations. Anti-hallucination — every reference verified via API before inclusion. Generates BibTeX entries.

present-paper

Academic presentation preparation — paper-driven (journal club, grand rounds, seminar) and lecture/teaching decks (course material, workshop slides, conference talks). Analyzes source material, finds supporting references, drafts audience-adapted speaker…

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.

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…

orchestrate

General-purpose research orchestrator. Routes ambiguous or multi-step requests to the right skill(s) from the medsci-skills bundle. Use when the user describes a research goal without naming a specific skill, or when a task spans multiple skills.

obsidian-paper-vault

Turn a folder of research PDFs into an Obsidian knowledge vault — consistently formatted literature notes with frontmatter, PDF embed links, and cross-referenced atomic concept notes. Use whenever the user wants PDFs converted to Obsidian notes, a batch of…

model-validation

Design or audit the clinical-validation study for an engineer-built medical-imaging model (segmentation, classification, or detection) before the validation report or manuscript is written. Covers patient-level split disjointness and the data-leakage…

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 /…

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 —…

verify-refs

Audit-only verification of manuscript references against PubMed and CrossRef. Detects fabricated or mismatched citations and writes qc/reference_audit.json. Does not modify references/ or refs.bib.

preprocess-imaging

Design or audit the data-preparation stage of a medical-imaging model — DICOM/NIfTI intake, resampling and intensity normalisation, and the augmentation plan — so the pipeline is leakage-safe before model-scaffold builds the training repo. Emits a declarative…

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.…

polish-language

Academic English consistency linting and non-native (ESL) language polish for medical manuscripts. Deterministically flags abbreviation define-once violations, US/UK spelling drift, hyphen-vs-en-dash numeric ranges, P/p case, hyphenation variants,…

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…

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…

render-pdf-doc

Render academic Markdown documents (English or Korean) to publication-quality PDF via pandoc + xelatex. Targets non-bibliography artifacts: research proposals, IRB cover letters, briefing handouts, anchor docs (Q&A grids), and reference tables. Auto-infers…

revise

Parse peer reviewer comments and generate a structured Response to Reviewers document with tracked manuscript changes. Classifies comments as MAJOR/MINOR/REBUTTAL, coordinates new analyses with /analyze-stats and /make-figures, and produces cover letter for…

write-protocol

IRB/ethics committee research protocol generator. Produces 4 core sections (Background, Study Design, Sample Size, Statistical Plan) with full prose, plus 6 skeleton sections with TODO markers for institution-specific content. Integrates outputs from…

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,…

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.

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,…

model-sourcing

Vet the concrete third-party model a study will be built on — this repository, this revision, this checkpoint — not the architecture family. Records a model dossier (source and version pin, licence and the file it was read from, intended use,…

profile-imaging

Profile a medical-imaging dataset before any modelling decision is made — the acquisition grid, voxel spacing and orientation spread, the intensity domain, which label values are actually present, how much of the volume the target occupies, and how large the…

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,…

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.

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,…

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…

mllm-eval

Design or audit a model-agnostic evaluation harness for an LLM or multimodal LLM on a clinical task (radiology report generation, visual question answering, clinical text extraction/classification) — the adjudicated reference standard, clinical-efficacy…

model-card

Generate the documentation an engineer-built medical-imaging model must carry — a Model Card (Mitchell et al. 2019), a Datasheet for its dataset (Gebru et al. 2021), and a METRIC-informed data-quality pass — filled from user-supplied facts, then verify every…

model-evaluation

Compute and report task-correct held-out metrics for a trained medical-imaging model — segmentation (Dice plus a boundary metric such as HD95 or NSD, per structure), classification (AUROC plus AUPRC and sensitivity/specificity with bootstrap CIs at the…