「boundary」の検索結果

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. Orchestrates temporal DE (limma splines or DESeq2 LRT), Mfuzz/tslearn soft clustering of expression-profile shapes, GAM trajectory fitting, per-cluster GO enrichment against a temporal-gene background, and an OPTIONAL circadian rhythm-detection branch (MetaCycle/CosinorPy) that runs only when the design covers >=2 full cycles with >=6-8 evenly spaced samples per cycle. Use when analyzing a bulk time-series expression experiment from any omics platform and deciding limma-splines vs DESeq2-LRT for temporal DE, soft vs hard clustering, whether the sampling design even licenses rhythm detection, and which background to use for enrichment. Not for single-cell pseudotime (see temporal-genomics/trajectory-modeling for the bulk-vs-pseudotime boundary) or unknown-period discovery (see temporal-genomics/periodicity-detection).

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。

Walk every branching path and boundary condition in content, report only unhandled edge cases. Orthogonal to adversarial review - method-driven not attitude-driven. Use when you need exhaustive edge-case analysis of code, specs, or diffs.

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。

Use when you need to design, review, or improve REST APIs with Spring Boot — including HTTP methods, resource URIs, status codes, DTOs, versioning, deprecation and sunset headers, content negotiation (JSON and vendor media types), ISO-8601 instants in DTOs, pagination/sorting/filtering, Bean Validation at the boundary, idempotency, ETag concurrency, HTTP caching, error handling, security, contract-first OpenAPI (OpenAPI Generator), controller advice, and problem details for errors. This should trigger for requests such as Review Java code for Spring Boot REST API; Apply best practices for Spring Boot REST API in Java code. Part of cursor-rules-java project

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。

Ensure designs define trust boundaries, authn/authz responsibilities, and propagation of identity/claims across services.

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。

Ensure designs define data flow, state ownership, consistency boundaries, and cross-boundary writes to prevent drift and incidents.

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。

Checks whether AI-assisted work defines review criteria, accessible context, explicit review loop, human judgment boundary, and feedback capture before delegating to an agent.

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。

Detect review findings that belong in CI/lint/formatter rather than human review.

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。

App Router の Server Component でクライアント専用APIを使っていないか確認する。

Checks React Router v7 action conventions: validation errors returned as data with 4xx status (not thrown), redirect on success, and 3-branch ErrorBoundary handling.

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。

Detects route data fetched in useEffect instead of loaders, server/client API leaks across loader boundaries, and missing HydrateFallback in React Router v7 framework mode.

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。

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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。

Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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。

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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。

Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.

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。

Builds reusable Convex components with isolated tables and app-facing APIs. Use for new components, reusable backend modules, integrations, or component boundary work.

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。

Design traceable functional test conditions across positive, negative, boundary, and error behavior with observable expectations.

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。

Clear the freeze boundary set by /freeze, allowing edits to all directories again. Use when you want to widen edit scope without ending the session. Use when asked to "unfreeze", "unlock edits", "remove freeze", or "allow all edits". (gstack)

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。

Pre-landing PR review. Analyzes diff against the base branch for SQL safety, LLM trust boundary violations, conditional side effects, and other structural issues. Use when asked to "review this PR", "code review", "pre-landing review", or "check my diff". Proactively suggest when the user is about to merge or land code changes. (gstack)

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。

Explain Ponytail's intended tradeoffs and measurement boundary. It does not estimate code, cost, or speed savings for the current repository. One-shot display, not a persistent mode. Trigger: ponytail-gain, "ponytail gain", "what does ponytail save", "show ponytail impact", or "ponytail scoreboard".

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。

Plan which model tier handles which work BEFORE execution begins — a high-cognition model deeply understands the problem, lays the foundations, then emits a modular plan assigning each module the cheapest tier that can safely execute it, with escalation tripwires and one-way-door protection. Advisory only: it announces "next module → tier X / model Y" at each boundary and the HUMAN switches models — harnesses like Cursor cannot switch mid-run. Load when the user asks which model to use, wants a model plan, model tiers, model-tier routing, assign models to tasks or modules, says "cheap model got stuck", "which model for this task", "cost-efficient model choice", or when implementation-plan / problem-to-plan need a model: tier column. NOT dynamic-routing (plan-path selection after failure) — this skill assigns cognition tiers to work.

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。

Capture the "why" behind technical choices to prevent architectural drift. Load when the user makes a major technical decision, chooses a library/framework, defines a system boundary, or changes a core architectural pattern. Also triggers on "record a decision", "write an ADR", "why did we do this", "document this architectural choice", or "architectural decision record". Supports `SYNTHESIS=true` mode for retrospective ADR backfill from observed repo state — used by `retroactive-project-setup` and any future backfill skill. Essential for long-term project maintainability and agent alignment.

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。

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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。

Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates, flowDensity data-driven thresholds, flowClust model-based gates), organized as a hierarchical GatingSet (flowWorkspace) and round-tripped with FlowJo via CytoML. Covers the canonical gate order (time -> debris -> singlets -> live -> lineage), FMO-vs-isotype boundary setting, gate-order dependence and recompute semantics, rare-event/MRD gating, and per-population statistics. Use when building a gating strategy, automating a manual FlowJo scheme across samples, choosing manual vs data-driven gates, or extracting population frequencies.

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。

Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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。