「failure」の検索結果

Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental designs each is built for, failure modes outside design domain, reconciliation when methods disagree, multiple-testing and effect-size thresholds, the order of operations (count -> QC -> CN-correct -> hit-call -> validate), the second-best-sgRNA conservative rule, and consensus-hit strategy. Use when choosing among MAGeCK / BAGEL2 / drugZ / JACKS / Chronos for a given design, reconciling disagreement across two or three methods on the same screen, deciding whether to require consensus, gating downstream validation by hit-confidence tier, or interpreting unstable hit lists across reruns.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Testing patterns for PHPUnit and Playwright E2E tests. Use when writing tests, debugging test failures, setting up test coverage, or implementing test patterns for ActivityPub features.

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Assesses the patient’s ability to troubleshoot insulin pump malfunctions such as occlusion, battery failure, or error messages. Trigger phrases include “Review pump alarm responses” and “Ensure patient knows steps for pump error”.

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Guides comorbidity-stratified selection of initial and further glucose-lowering medicines for adults with type 2 diabetes using the NICE NG28 (2026) framework, covering six clinical profiles: no relevant comorbidity, heart failure, atherosclerotic cardiovascular disease, early onset, obesity, chronic kidney disease, and frailty.

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Execute a swarm plan wave by wave with filesystem isolation via git worktrees. For each wave, main context decides the scenario recipe + implementation contract for every task, then spawns one swarm-worker per task in parallel. Each worker executes its recipe and reports JSON status. Worktree merge-audit verifies write-set discipline before changes land on main. Aborts remaining waves on any audit or task failure.

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Draft a Root Cause Analysis for an incident, outage, or repeated test failure. Unlike intake/spec/brd, RCA is not a workflow phase — it's a standalone postmortem artifact that often precedes a bugfix intake. Output lives at `docs/rca/<slug>.md`.

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Capture what someone actually said without contaminating it with your own inference. Invoke when eliciting intent in conversation (design discussion, requirement interview, decision surfacing) and when turning a conversation into a durable record (ADR, decision node, memory entry, spec `## Decisions` row). Enforces quote-before-critique, keeps illustration separate from commitment, and holds interpretation subordinate to verbatim. Prevents the failure where unspecified space is filled by the recorder and then evaluated as if the speaker had specified it.

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Dev-only review of user-facing CLI interface copy in `src/cli/tui/*.js`, `src/cli/*.js` error paths, and `bin/cli.js` help/usage text. Surfaces three failure modes — copy/behavior mismatch, jargon, missing next-action — as a punch list the maintainer addresses before `/grant-commit`. Read-only; no writes to source. Conditionally seeded by `/triage` between `/memory-sync` and `/grant-commit` when the request will touch CLI surfaces.

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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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Autonomous experiment loop that optimizes any file by a measurable metric. Inspired by Karpathy's autoresearch. The agent edits a target file, runs a fixed evaluation, keeps improvements (git commit), discards failures (git reset), and loops indefinitely. Use when: user wants to optimize code speed, reduce bundle/image size, improve test pass rate, optimize prompts, improve content quality (headlines, copy, CTR), or run any measurable improvement loop. Requires: a target file, an evaluation command that outputs a metric, and a git repo.

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Autonomous agents are AI systems that can independently decompose goals, plan actions, execute tools, and self-correct without constant human guidance. The challenge isn't making them capable - it's making them reliable. Every extra decision multiplies failure probability.

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Audit local AI coding-agent sessions with agenttrace for cost, tool failures, latency, anomalies, health, diffs, and CI gates.

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Design production-grade multi-agent workflows with clear pattern choice (sequential, parallel, hierarchical), handoff contracts, failure handling, and cost/context controls. Use when architecting a multi-step agent pipeline, choosing between single-agent vs multi-agent approaches, or refactoring an LLM workflow that suffers from context bloat or unreliable handoffs.

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Use when the user asks to design a multi-agent system, pick an orchestration pattern (supervisor/swarm/pipeline), generate tool schemas for agents, or evaluate agent execution logs for cost, latency, and failure bottlenecks. Examples: 'design an agent architecture for research automation', 'generate Anthropic tool schemas from these tool descriptions', 'analyze these agent run logs for bottlenecks'. NOT for Claude Code workflow files (use workflow-builder) or single-agent prompt design (use agent-workflow-designer).

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Act as a senior Amazon account growth operator that combines Amazon performance-drop analytics, Amazon growth-opportunity analytics, Amazon Ads data, retail readiness, BSR/rank signals, margin, inventory, and campaign/search-term evidence into a prioritized profitable growth action plan. Use when Codex needs to decide what to protect, fix, scale, reduce, pause, harvest, launch, or monitor for an Amazon brand, agency, marketplace, ASIN set, or account; when building daily, weekly, or monthly Amazon account operating plans; when reallocating ad budget; when deciding which ASINs are safe or risky to push; or when turning performance-drop and growth-opportunity findings into approval-gated actions with success/failure criteria.

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Test a changed user interaction for realistic sequence failures such as double submission, stale responses, navigation, and recovery; use for interaction QA rather than general code review.

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Use for the 5 Whys, or when the user wants the root cause of a failure: "why did this happen?", "this keeps breaking", "write the postmortem", "find the real cause". Asks why repeatedly with evidence at each step, then sets countermeasures. Skip for one-off typos or when the cause is already proven.

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Build or modify backend APIs, services, jobs, persistence, and integrations while preserving contracts, authorization, data integrity, and failure behavior. Use for server-side features, database changes, background processing, backend defects, and service refactors; do not use for frontend-only or infrastructure-only work.

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