aperivue/medsci-skills
57 skills · 1,096 total installs
$npx skills add aperivue/medsci-skillsSkillInstalls
meta-analysisSystematic 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), stanalyze-statsStatistical analysis for medical research papers. Generates reproducible Python/R code with publication-ready tables and figures. Supports diagnostic accuracy, inter-rater agreement, meta-analysis, sumake-figuresGenerate 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, Blanfind-cohort-gapResearch 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 anhumanizeDetect and remove AI writing patterns from academic manuscripts and response-to-reviewers letters. Scans for 26 common AI-generated text patterns and rewrites flagged passages to sound naturally humanself-reviewPre-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 Commentsma-scoutMeta-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.orchestrateGeneral-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 specifiwrite-paperFull-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 fulltext-retrievalBatch download open-access PDFs by DOI using legitimate OA APIs (Unpaywall, PMC, OpenAlex, Crossref). Optional PDF→Markdown conversion for token-efficient LLM analysis.grant-builderGrant and challenge proposal support for radiology and medical AI projects. Structures significance, innovation, approach, milestones, and consortium roles while keeping claims evidence-based and execintake-projectIntake and normalize a new radiology research project. Classifies project type, summarizes current state, identifies missing inputs, recommends next steps, and scaffolds lightweight project memory filpresent-paperAcademic presentation preparation — paper-driven (journal club, grand rounds, seminar) and lecture/teaching decks (course material, workshop slides, conference talks). Analyzes source material, finds render-pdf-docRender academic Markdown documents (English or Korean) to publication-quality PDF via pandoc + xelatex. Targets non-bibliography artifacts: research proposals, IRB cover letters, briefing handouts, anreviseParse 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 /analysearch-litLiterature search and citation management for medical research. Searches PubMed, Semantic Scholar, and bioRxiv/medRxiv with verified citations. Anti-hallucination — every reference verified via API beverify-refsAudit-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.write-protocolIRB/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 inslit-syncSync 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.manage-refsCross-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]`` replicate-studyReplicate an existing cohort study's methodology on a different database. Extracts study design from a source paper, maps variables to the target DB via harmonization table, generates analysis code, async-submissionAudit SSOT-to-submission drift and create journal submission manifests from canonical manuscript artifacts.setup-medsciDiagnostic checklist for the MedSci Skills runtime. Verifies Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers, and prints a pass/fail table with links to the right setup doc for apolish-languageAcademic 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 generate-codebookGenerate 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, misreview-paperScaffold and draft medical/AI literature reviews (narrative, scoping PRISMA-ScR, or systematic). Asks for the spine axis, builds a 7-part skeleton with a required Intro scope/non-overlap block, a summversion-datasetDataset version control for research reproducibility. Builds a deterministic content-hash manifest of a dataset (file SHA-256 + tabular schema + per-column value hashes), verifies a later copy againstacademic-aioMedical 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, structuadd-journalAdd 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 qualityarchitecture-zooChoose a model architecture for a medical-imaging research question before scaffolding. Maps the task (classification, segmentation, detection, transfer), modality and dimensionality, labelled-data scauthor-strategyPubMed author profile analysis. Author name → PubMed fetch → study-type classification → visualization → strategy report → optional trajectory-archetype classification.batch-cohortGenerate 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/Pytcalc-sample-sizeInteractive sample size calculator for medical research. Decision-tree guided test selection, reproducible R/Python code, effect size interpretation, and IRB-ready justification text. Supports diagnoscheck-reportingCheck manuscript compliance with medical research reporting guidelines. Supports 46 guidelines including STROBE, STROBE-MR, RECORD, REMARK (prognostic tumor-marker studies), TARGET (target trial emulaclean-dataInteractive 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, dupcontributeOffer 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 gicross-nationalEnd-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+define-variablesLiterature-grounded variable operationalization for observational research. Turns a data dictionary + research question into a citation-backed table of exposure/outcome/covariate definitions, cutoffs,deidentifyDe-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). Interacdesign-ai-benchmarkingDesign 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-dimensiondesign-studyStudy 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 beforexplainabilityProduce 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 refill-icmje-coiBatch-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 sfill-protocolFill institutional Word form templates (.doc/.docx) for IRB protocols, ethics applications, grant proposals, and other structured research documents while preserving the original styles, table layoutsfind-journalJournal 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 tomanage-projectResearch project management for medical manuscripts. Scaffold project structure, track writing progress across phases, maintain project memory files, generate submission checklists and backwards timelmllm-evalDesign 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) — model-cardGenerate 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-qualitymodel-evaluationCompute 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 amodel-scaffoldGenerate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation, classification, detection, image-to-image synthesis, self-supervised pretraining, or fine-tuning a prmodel-validationDesign 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 patpeer-reviewPeer review assistant for medical journals. Generates structured review drafts with journal-specific formatting. Constructive developmental tone with systematic manuscript analysis.preprocess-imagingDesign 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 mprofile-imagingProfile 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, howpublish-skillConvert 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.radiomics-mlProduce or audit a radiomics / tabular clinical-ML study — imaging or clinical features → any classical learner (penalised logistic [LASSO / ridge / elastic-net], SVM, k-NN, naive Bayes, LDA/QDA, deciuncertainty-imagingDesign or audit the uncertainty-quantification, out-of-distribution (OOD) detection, and selective-prediction layer of a medical-imaging model framed for deployment — so a clinical-use claim carries c