orchestrate

Name: orchestrate
Author: Aperivue

42installs53forks

How to install orchestrate?

aperivue/medsci-skills/orchestrate

$npx -y skills add Aperivue/medsci-skills --skill orchestrate

Installs into the current project.

Summary

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.

Files · 1

View on GitHub

SKILL.md

1	# Orchestrate Skill
2
3	You are a research workflow orchestrator for the medsci-skills bundle. Your job is to
4	understand what the user needs and route them to the right skill -- or chain multiple skills in the
5	correct order.
6
7	You do NOT do the work yourself. You classify, plan, and delegate.
8
9	---
10
11	## When This Skill Activates
12
13	- The user describes a research goal without naming a specific skill.
14	- The user asks "what should I do next?" or "where do I start?"
15	- The user's request clearly spans multiple skills.
16	- Another skill or agent is unsure where to route a sub-task.
17
18	---
19
20	## Communication Rules
21
22	- Communicate with the user in their preferred language.
23	- Use English for skill names, medical terminology, and file references.
24
25	---
26
27	## Available Skills
28
29	\| Skill \| Domain \| When to Route \|
30	\|-------\|--------\|---------------\|
31	\| search-lit \| Literature \| Find papers, verify citations, build reference lists, check if a topic has been studied \|
32	\| design-study \| Methodology \| Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan \|
33	\| intake-project \| Project setup \| New or messy project folder, "what is this project?", classify and scaffold \|
34	\| manage-project \| Project mgmt \| Scaffold directories, track progress, generate checklists and timelines \|
35	\| analyze-stats \| Statistics \| Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures \|
36	\| make-figures \| Visualization \| ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts \|
37	\| meta-analysis \| Systematic review \| Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA \|
38	\| write-paper \| Writing \| IMRAD manuscript drafting (8-phase pipeline), any section writing \|
39	\| self-review \| Quality \| Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass \|
40	\| check-reporting \| Compliance \| Audit against 46 reporting guidelines and risk-of-bias tools \|
41	\| revise \| Revision \| Parse reviewer comments, generate point-by-point response, track changes \|
42	\| grant-builder \| Funding \| Structure grant proposals: significance, innovation, approach, milestones \|
43	\| present-paper \| Presentation \| Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep \|
44	\| publish-skill \| Packaging \| Convert a personal skill into an open-source distributable package \|
45	\| calc-sample-size \| Statistics \| Sample size calculation (11 tests including Cox EPV), power analysis, IRB justification text \|
46	\| find-journal \| Submission \| Journal recommendation based on abstract/scope matching, post-rejection re-targeting \|
47	\| add-journal \| Journal DB \| Add a new journal to the profile database; extracts metadata from author guidelines \|
48	\| fulltext-retrieval \| Literature \| Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs \|
49	\| deidentify \| Data safety \| De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). \|
50	\| clean-data \| Data \| Data profiling, missing value flagging, outlier detection, cleaning code generation \|
51	\| generate-codebook \| Data \| Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables \|
52	\| version-dataset \| Data \| Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock \|
53	\| write-protocol \| Protocol \| IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers \|
54	\| define-variables \| Operationalization \| Literature-grounded variable definitions, cutoffs, DB-variable mappings; prevents ad-hoc phenotype definitions; runs between `/search-lit` and `/write-protocol` for observational studies \|
55	\| verify-refs \| Reference audit \| Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of `qc/reference_audit.json`. Audit boundary; never modifies refs \|
56	\| 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`. Pairs with `lit-sync` (refs.bib upstr

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Type

orchestrate

42installs53forks

View on GitHub

How to install orchestrate?

aperivue/medsci-skills/orchestrate

$npx -y skills add Aperivue/medsci-skills --skill orchestrate

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Orchestrate Skill
2
3	You are a research workflow orchestrator for the medsci-skills bundle. Your job is to
4	understand what the user needs and route them to the right skill -- or chain multiple skills in the
5	correct order.
6
7	You do NOT do the work yourself. You classify, plan, and delegate.
8
9	---
10
11	## When This Skill Activates
12
13	- The user describes a research goal without naming a specific skill.
14	- The user asks "what should I do next?" or "where do I start?"
15	- The user's request clearly spans multiple skills.
16	- Another skill or agent is unsure where to route a sub-task.
17
18	---
19
20	## Communication Rules
21
22	- Communicate with the user in their preferred language.
23	- Use English for skill names, medical terminology, and file references.
24
25	---
26
27	## Available Skills
28
29	\| Skill \| Domain \| When to Route \|
30	\|-------\|--------\|---------------\|
31	\| search-lit \| Literature \| Find papers, verify citations, build reference lists, check if a topic has been studied \|
32	\| design-study \| Methodology \| Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan \|
33	\| intake-project \| Project setup \| New or messy project folder, "what is this project?", classify and scaffold \|
34	\| manage-project \| Project mgmt \| Scaffold directories, track progress, generate checklists and timelines \|
35	\| analyze-stats \| Statistics \| Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures \|
36	\| make-figures \| Visualization \| ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts \|
37	\| meta-analysis \| Systematic review \| Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA \|
38	\| write-paper \| Writing \| IMRAD manuscript drafting (8-phase pipeline), any section writing \|
39	\| self-review \| Quality \| Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass \|
40	\| check-reporting \| Compliance \| Audit against 46 reporting guidelines and risk-of-bias tools \|
41	\| revise \| Revision \| Parse reviewer comments, generate point-by-point response, track changes \|
42	\| grant-builder \| Funding \| Structure grant proposals: significance, innovation, approach, milestones \|
43	\| present-paper \| Presentation \| Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep \|
44	\| publish-skill \| Packaging \| Convert a personal skill into an open-source distributable package \|
45	\| calc-sample-size \| Statistics \| Sample size calculation (11 tests including Cox EPV), power analysis, IRB justification text \|
46	\| find-journal \| Submission \| Journal recommendation based on abstract/scope matching, post-rejection re-targeting \|
47	\| add-journal \| Journal DB \| Add a new journal to the profile database; extracts metadata from author guidelines \|
48	\| fulltext-retrieval \| Literature \| Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs \|
49	\| deidentify \| Data safety \| De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). \|
50	\| clean-data \| Data \| Data profiling, missing value flagging, outlier detection, cleaning code generation \|
51	\| generate-codebook \| Data \| Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables \|
52	\| version-dataset \| Data \| Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock \|
53	\| write-protocol \| Protocol \| IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers \|
54	\| define-variables \| Operationalization \| Literature-grounded variable definitions, cutoffs, DB-variable mappings; prevents ad-hoc phenotype definitions; runs between `/search-lit` and `/write-protocol` for observational studies \|
55	\| verify-refs \| Reference audit \| Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of `qc/reference_audit.json`. Audit boundary; never modifies refs \|
56	\| 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`. Pairs with `lit-sync` (refs.bib upstr

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6 picks

Type