Claude Code Commands

Clinical study design. Select and classify endpoints, estimate sample size / power (means / proportions / survival), and score a study plan for a GO. Slash command for Claude Code, Codex CLI, Gemini CLI.

Clinical study design. Select and classify endpoints, estimate sample size / power (means / proportions / survival), and score a study plan for a GO / GO-WITH-CONDITIONS / REDESIGN / NO-GO phase-gate decision. Every output is an ESTIMATE plus a named clinical owner — never clinical fact. Direct invocation of the clinical-research skill.

/cs:deep-research <question> — Disciplined multi-source investigation for a high-stakes question. Reframes into falsifiable hypotheses, plans, fans out parallel search sub-agents, triangulates every thesis against >=3 independent sources, saves each source to its own file with verbatim quotes, runs an adversarial pass, and emits an auditable, reusable research folder with a refresh protocol. The heavyweight alternative to the fast research router.

/cs:grants <research-idea> — NIH funding intelligence. 6-Q grill-me intake (idea + career stage + prelim + environment + posture + institutes) → 5-facet Consensus positioning + RePORTER POST institute mapping + NOSI fetches → 9-section .docx with mandatory program officer recommendation.

/cs:grants <research-idea> — NIH funding intelligence. 6-Q grill-me intake (idea + career stage + prelim + environment + posture + institutes) →. Slash command for Claude Code, Codex CLI, Gemini CLI.

Matt Pocock-style docs-anchored grilling for a Research Operations plan — clinical study, R&D budget, market size, or product study. Walks the plan against the research canon (ICH E9, IAS 38, Cochran, Kotler, Nielsen) one question at a time, recommends an answer per question, and refuses to invoke any sub-skill until the lane-defining decisions are locked. Use before running /cs:research-ops on a fuzzy plan.

Matt Pocock-style docs-anchored grilling for a Research Operations plan — clinical study, R&D budget, market size, or product study. Walks the plan. Slash command for Claude Code, Codex CLI, Gemini CLI.

/cs:litreview <research-question> — Academic literature orientation. Grill-me intake (question + framework + depth), Consensus recon, framework. Slash command for Claude Code, Codex CLI, Gemini CLI.

/cs:litreview <research-question> — Academic literature orientation. Grill-me intake (question + framework + depth), free-lane recon (PubMed E-utilities + OpenAlex, keyless; Consensus MCP added only when connected), framework checkpoint, sequential budget-allocated searches (5/10/20), 8-section .docx research guide output. Sibling of /cs:pulse (research pack).

/cs:patent <invention> — Patent prior-art + landscape intelligence with mandatory sub-use-case commitment. 6-Q grill-me intake (Q2 picks one of: novelty / FTO / landscape / diligence / litigation). Multi-source search (Google Patents + Espacenet + USPTO + optional Lens.org BYOK). 8-section .docx with verdict + claim text + family-resolved hits + mandatory legal disclaimer (novelty + FTO).

/cs:patent <invention> — Patent prior-art + landscape intelligence with mandatory sub-use-case commitment. 6-Q grill-me intake (Q2 picks one of. Slash command for Claude Code, Codex CLI, Gemini CLI.

Product / user research methodology. Select the right method for the goal (generative vs evaluative vs validation), compute method-based saturation /. Slash command for Claude Code, Codex CLI, Gemini CLI.

Product / user research methodology. Select the right method for the goal (generative vs evaluative vs validation), compute method-based saturation / sample size with an explicit confidence level, and synthesize coded observations into insights while flagging single-source anecdotes. Never fabricates insight. Direct invocation of the product-research skill.

/cs:research <question> — Default research entry point. Hybrid router: classifies question deterministically and either delegates to specialist. Slash command for Claude Code, Codex CLI, Gemini CLI.

/cs:research <question> — Default research entry point. Hybrid router: classifies question deterministically and either delegates to specialist (pulse / grants / litreview / dossier / patent / syllabus) OR runs own plan-decompose-search-synthesize fallback. Always surfaces routing decision; accepts override. NEVER silent delegation.

R&D program finance. Build a multi-period program budget with the F&A (indirect) split, track burn rate and runway against value-inflection milestones, and route R&D cost items to a capitalize-vs-expense determination. Every budget surfaces its assumptions; capex-vs-opex routes to a named finance owner and never auto-decides. Direct invocation of the research-finance skill.

R&D program finance. Build a multi-period program budget with the F&A (indirect) split, track burn rate and runway against value-inflection. Slash command for Claude Code, Codex CLI, Gemini CLI.

Top-level Research Operations router. Classifies an enterprise research inquiry (clinical study design / R&D finance / market research / product research) and forks context to the right sub-skill via the research-ops-skills orchestrator, returning a ≤200-word digest with a named owner and one grill challenge.

Top-level Research Operations router. Classifies an enterprise research inquiry (clinical study design / R&D finance / market research / product. Slash command for Claude Code, Codex CLI, Gemini CLI.

Search the KEGG bioinformatics database for pathways, genes, compounds, drugs, enzymes, or diseases

Investigate a drug — targets, pathways, classification, and interactions

Deep-dive into a KEGG pathway — genes, compounds, reactions, and ASCII visualization

Run Rigor Explore on top of current_research using the current compatible slug.

Run Rigor Reproduce on this repository using the current compatible slug.

Run Rigor Debug on a research repository failure before patching.