「gate」の検索結果

The last gate before merge — QA, security audit, review and changelog, with objective pass conditions.

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Navigate your projects. Get context, paths, status. Use when needing project overview or finding specific work.

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Enter explore mode - think through ideas, investigate problems, clarify requirements

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Resolve a verified cluster of Rembric issues from causal root to evidence-gated closure. Use after systemic triage identifies a shared root, or when the user asks to attack issues at the root, create a mechanism map, plan a deletion-first fix, or close a fixed/stale issue cluster. Use `diagnose` for a single defect whose reproduction is not yet established.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, mixed), Hochberg/Hommel/Holm with PRDS, and the closed-testing principle (Marcus-Peritz-Gabriel; Goeman 2021 admissibility). Covers FDA Multiple Endpoints Final Guidance (October 2022), graphical procedures via R gMCP, primary + key-secondary + subgroup hierarchies, and FWER vs FDR distinction. Use when designing the multiplicity strategy for confirmatory trials with multiple primary or key secondary endpoints.

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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Calculate the Maryland Aggregate Pathology Index (MAPI) on a deceased donor procurement kidney biopsy to predict graft survival and decide single vs dual vs discard allocation. Trigger when a clinician asks "what's the MAPI score", "interpret donor kidney biopsy", "should I use this marginal kidney", "MAPI cutoff for transplant", "procurement biopsy scoring", or has histology results from a deceased donor kidney and needs an objective grading.

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Standard operating procedure for producing a documentation page end to end — gather source material, classify, draft against the measured corpus profile, then run the reader-level and humanizer passes and both gates. Use for any page on a documentation surface, or when rewriting a page that reads as machine-written. Orchestrates technical-writing, reader-level and humanizer in a fixed order.

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End-to-end workflow orchestrator. Walks the 11-phase pipeline, invoking each phase skill in order inside an internal loop, yielding at consent gates (/approve-direction, /approve-swarm, /grant-commit), and exiting cleanly on yield/failure/done. Decides swarm-vs-solo at Phase 6. Auto-loops /tdd on integrate failures that don't require a spec change. The harness_continuation Stop hook is a safety net that re-fires harness only when the loop exited mid-flow.

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Workflow Phase 3 — Research and Solution Exploration. Surfaces 2–4 candidate solution approaches with concrete tradeoffs, grounded in current library docs (fetched through the provider named in `.claude/docs-provider.json`) — never in training-data recall. Output lives at `docs/research/<slug>.md`. Candidate ranking and the memo execute in main context; doc/source gathering MAY be delegated to read-only advisory subagents (seed.md §4.2-A).

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Workflow Phase 2 — Codebase Scouting and Constraint Discovery. Maps the relevant slice of the codebase for a given task. Produces a scout report at `docs/scout/<slug>.md` naming the files, modules, and patterns the proposed work touches or constrains. Report decisions execute in main context with full conversation visibility; gathering MAY be delegated to read-only advisory subagents (seed.md §4.2-A).

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Dev-only check that a drafted spec for THIS baseline repo won't ship dev-tree references to consumer installs. Catches three failure modes — shipped SKILL.md prose that references paths under `src/`, `tests/`, `scripts/`, `obj/` as runtime invocations (in ```bash fences``` OR `inline backticks`, plus shipped `.mjs`/`.js`/`.sh`/`.py` helper-file imports); new Python helpers added under `.claude/skills/<slug>/` (shipped helpers must be `.sh` or `.mjs`/`.js` going forward); and imports of modules that aren't in `obj/template/.claude/manifest.json` (consumer won't have the file). The aggregate scanner (`scan-shipped-skills.mjs`) walks only baseline-owned skill dirs (via `owner: baseline` frontmatter) at top level — `references/` and other subdirs are documentation, not runtime. BLOCKER findings hard-block implementation entry; ADVISORY surfaces but doesn't block. Read-only — surfaces a punch list; maintainer edits the spec and re-runs until CLEAN.

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The sprint completeness oracle — a mechanical, exit-code-driven check that every feature in a sprint manifest is provably complete across three dimensions (a done-record reference, resolvable edge tests, and a resolvable wiring test). Fails loud with a per-feature gap list naming the missing dimension. Read-only. Use to gate a sprint before it is called done (Slice A of the sprint-mode epic), or any time you want a completeness reading.

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Cycle-end retrospective converting recurring judgment failures into durable enforcement. Reviews the cycle's friction — repeated user corrections, guard trips, RCA themes, integrate failures — and turns each recurring one into a landmines.md entry, then proposes graduation candidates up the enforcement funnel (landmine → advisory hook → hard gate). Pairs with standup: standup says what shipped and what's next; retrospective says what kept going wrong and how to stop it structurally. Writes only memory entries and a report — graduation proposals are advisory and require the normal seed.md amendment path to become enforcement. Invoke at the end of a release cycle, an epic, or any stretch of work with repeated friction.

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Automates browser interactions for web testing, form filling, screenshots, and data extraction. Use when the user needs to navigate websites, interact with web pages, fill forms, take screenshots, test web applications, or extract information from web pages.

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Execute plans via delegate_task subagents (2-stage review).

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Pre-commit review: security scan, quality gates, auto-fix.

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Debug Hermes TUI slash commands: Python, gateway, Ink UI.

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Delegate coding to Claude Code CLI (features, PRs).

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Automates CI/CD pipeline setup. Use when setting up or modifying build and deployment pipelines. Use when you need to automate quality gates, configure test runners in CI, or establish deployment strategies.

日本語の概要は準備中です。原文の説明を表示しています。