aperivue/medsci-skills/orchestrate
Trust tier 2
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Use when the user describes a research goal without naming a skill, or the task spans several skills. Classifies the request, plans the order and routes to the right medsci-skills skill(s) instead of producing their output itself.
Install
npx vskill@latest install aperivue/medsci-skills/orchestrateSKILL.md
Orchestrate Skill
Route research requests in the medsci-skills bundle to the right skill, or chain several skills in the correct order. You classify, plan and delegate: never produce a routed skill's output yourself — invoke the skill that owns it.
Available Skills
| Skill | Domain | When to Route | |
|---|---|---|---|
| search-lit | Literature | Find papers, verify citations, build reference lists, check if a topic has been studied | |
| design-study | Methodology | Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan | |
| intake-project | Project setup | New or messy project folder, "what is this project?", classify and scaffold | |
| manage-project | Project mgmt | Scaffold directories, track progress, generate checklists and timelines | |
| analyze-stats | Statistics | Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures | |
| make-figures | Visualization | ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts | |
| meta-analysis | Systematic review | Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA | |
| write-paper | Writing | IMRAD manuscript drafting (8-phase pipeline), any section writing | |
| self-review | Quality | Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional --panel for a high-stakes final QC pass | |
| check-reporting | Compliance | Audit against 49 reporting guidelines and risk-of-bias tools | |
| revise | Revision | Parse reviewer comments, generate point-by-point response, track changes | |
| grant-builder | Funding | Structure grant proposals: significance, innovation, approach, milestones | |
| present-paper | Presentation | Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep | |
| publish-skill | Packaging | Convert a personal skill into an open-source distributable package | |
| calc-sample-size | Statistics | Sample size calculation (17 tests including Cox EPV), power analysis, IRB justification text | |
| find-journal | Submission | Journal recommendation based on abstract/scope matching, post-rejection re-targeting | |
| add-journal | Journal DB | Add a new journal to the profile database; extracts metadata from author guidelines | |
| fulltext-retrieval | Literature | Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs | |
| deidentify | Data safety | De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). | |
| clean-data | Data | Data profiling, missing value flagging, outlier detection, cleaning code generation | |
| generate-codebook | Data | Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables | |
| version-dataset | Data | Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock | |
| write-protocol | Protocol | IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers | |
| define-variables | Operationalization | Literature-grounded variable definitions, cutoffs, DB-variable mappings; runs between /search-lit and /write-protocol for observational studies | |
| verify-refs | Reference audit | Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of qc/reference_audit.json. Never modifies refs | |
| manage-refs | Reference lifecycle | Citekey validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, [N] ↔ [@key] marker conversion, Zotero CWYW field-code injection. Sole writer of manuscript_final.docx, qc/xref_audit.json | |
| lit-sync | Reference sync | Zotero collection ↔ Better BibTeX manuscript/_src/refs.bib ↔ Obsidian literature notes. Sole writer of refs.bib (auto-export); upstream of manage-refs | |
| obsidian-paper-vault | Vault build | A folder of PDFs → templated Obsidian literature notes + atomic concept notes synthesized across them. Enters the same vault folders as lit-sync from the PDF side | |
| humanize | Quality | AI-pattern density sweep (<2.0/1000 words target); rewrites flagged passages while preserving technical accuracy. Phase 7.5 of write-paper | |
| academic-aio | Visibility | AI-search-engine optimization for medical AI papers (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace, RAG tools). Opt-in checklist; never auto-applies edits | |
| render-pdf-doc | Document layout | Non-bibliography academic markdown → PDF (proposal, briefing, anchor doc, IRB cover, reference table), CJK-aware. Boundary opposite of manage-refs scripts/render_pandoc.sh | |
| fill-protocol | Form filling | Institutional Word form filling (.doc/.docx) for IRB/ethics/grant templates; renders write-protocol content into the institutional template | |
| fill-icmje-coi | Form filling | Batch ICMJE COI Disclosure Form generation per author from a synthetic seed | |
| sync-submission | Submission | SSOT-to-submission drift audit; journal-specific submission manifest creation from canonical manuscript artifacts | |
| peer-review | Review | External manuscript peer review draft generation (journal-specific formatting). Use ONLY for reviewing other authors' work, never for self-review | |
| review-paper | Writing | Scaffold/draft a literature review (narrative / scoping PRISMA-ScR / systematic). Distinct from write-paper (original research) and meta-analysis (pooling) | |
| polish-language | Quality | Academic-English consistency lint + non-native clarity polish (abbreviations, US/UK spelling, ranges, P/p case, units). Style-only; distinct from humanize (AI-tell removal) and check-reporting (guideline items) | |
| author-strategy | Analysis | PubMed author-profile analysis: study-type classification, trajectory-archetype, publication-strategy report from a name | |
| batch-cohort | Analysis | Generate N analysis scripts from one validated methodology template × many exposure/outcome combinations (same method, swap variables) + summary matrix | |
| replicate-study | Analysis | Replicate an existing cohort study's methodology on a different database: design extraction, variable-harmonization table, replication-difference report | |
| cross-national | Analysis | Cross-national comparison study (KNHANES + NHANES + CHNS or parallel surveys): variable harmonization + parallel weighted analysis | |
| ma-scout | Systematic review | Meta-analysis topic discovery + feasibility (professor-first profile→gap, or topic-first question→gap→co-author) before a protocol exists | |
| find-cohort-gap | Methodology | Research-gap discovery from a longitudinal cohort DB: profile strengths, match PI expertise, literature-saturation scan, ranked topic proposals | |
| design-ai-benchmarking | Methodology | Design/validity review for benchmarking AI systems against a human-expert reference panel (rubrics, calibration probes, panel construction, IRR targets) — before data collection | |
| model-selection | Modeling | Choose the model for an imaging study: a paper-grounded architecture family (task + modality + data scale + imbalance → shortlist), then vet the concrete repo / checkpoint (licence, version pin, weight provenance; flags an evaluation arm on the benchmark the model was developed or tuned on) | |
| imaging-data | Modeling | Profile an imaging dataset before any modelling decision (spacing/orientation, intensity domain, label integrity, foreground fraction, target volume) and gate it against the plan; then plan/audit DICOM/NIfTI intake, resampling, normalisation and augmentation with a preprocessing manifest + data-stage leakage gate before model-scaffold | |
| model-scaffold | Modeling | Generate a reproducible runnable PyTorch training repo (patient-level seed-locked split, task model, train/eval scripts, repro record) — between choosing an architecture and validating a trained model | |
| radiomics-ml | Modeling | Produce/audit a radiomics / tabular-ML study (imaging or clinical features → penalised logistic / SVM / RF / gradient-boosting / MLP → outcome) with a nested-CV / feature-stability / calibration / external-validation gate (no GPU) | |
| model-assessment | Validation | Validate/evaluate a trained imaging model: split-leakage gate + validation design (internal vs external, comparator, sizing); task-correct held-out metrics (Dice + boundary, AUROC + AUPRC with bootstrap CIs, FROC/mAP, calibration, subgroups) → per-case table; uncertainty/OOD/abstention for deployment claims; Grad-CAM/explainability sanity checks + localisation | |
| mllm-eval | Evaluation | Design/audit an evaluation harness for an LLM/MLLM clinical task (report generation, VQA, extraction/classification): adjudicated reference, clinical-efficacy metrics beyond BLEU/ROUGE, hallucination, contamination, prompt-sensitivity, reader study | |
| model-card | Documentation | Generate a Model Card + Datasheet + data-quality pass for an engineer-built imaging model from user-supplied facts, with a completeness gate | |
| contribute | Setup | Offer a local edit (a journal profile, a fix) back as a pull request or issue without typing git; blocks on patient data in the diff and sends nothing until confirmed. Also files a false positive or a failed step | |
| setup-medsci | Setup | Read-only runtime diagnostic (Python, R, Node, Claude Code, Git, Zotero, MCP servers): pass/fail table with the setup doc for each missing component |
Classification Logic
Classify each request into one of these intents.
Single-skill requests (route directly)
Route to the skill whose Available Skills row matches: name it with a one-line reason, then invoke it. The rows below cover modes and flags, look-alike skills, and non-English phrasings:
This is the start of the file. Read the full SKILL.md on GitHub.
Security
- Security scanPassed, 100 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryCheckingskills/orchestrate/SKILL.md
Popularity
- Repository stars
- 322
- Repository forks
- 78
- 7-day trend score
- 29
Stars and forks are for the whole GitHub repository, not this skill alone. Not refreshed yet.
Works with
Any agent vskill installs to: 56 targets in all. These 39 have a page on this site.
- Claude Code
- Cursor
- GitHub Copilot
- Windsurf
- Codex
- Gemini CLI
- Cline
- Amp
- Roo Code
- Goose
- Continue
- Kilo Code
- Junie
- Trae
- OpenHands
- Qwen Code
- AI Agent
- Tabnine Chat
- Sourcegraph Cody
- Amazon Q
- Firebase Genkit
- Sweep
- Devin
- Phind
- Mentat
- Claude Desktop
- Aider
- GPT Pilot
- Plandex
- bolt.new
- v0
- Replit Agent
- Anse
- TypingMind
- BetterChatGPT
- LibreChat
- Warp AI
- Pieces
- Fig AI
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