'failure' 검색 결과

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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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 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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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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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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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, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly 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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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

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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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Extract a thesis's dependency fingerprint — the external variables its bull case actually rests on (key customers, suppliers/inputs, technology transitions, macro drivers, single points of failure). Use when user says "dependency map", "what does [TICKER] depend on", "dependency fingerprint", or "map exposures for [TICKER]".

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Investigate implementation failures using root-cause-first debugging. Use when an implementer is blocked, verification fails, or repeated remediation does not converge.

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Use when encountering any bug, test failure, or unexpected behavior. 4-phase root cause investigation — NO fixes without understanding the problem first.

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Full pull request lifecycle — create branches, commit changes, open PRs, monitor CI status, auto-fix failures, and merge. Works with gh CLI or falls back to git + GitHub REST API via curl.

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Use when encountering any bug, test failure, or unexpected behavior, before proposing any fix

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Confiabilidade da plataforma — SLO, error budget, capacidade, resiliência, ponto único de falha e revisão de prontidão. Use quando o usuário disser "SLA", "SLO", "disponibilidade", "resiliência", "aguenta?", "single point of failure", "production readiness", "quanto de folga temos".

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Trace bugs backward through call stacks and execution flows to identify the original source of errors, invalid data, or incorrect behavior. Use when debugging complex issues, tracing error origins, investigating data corruption, following execution paths, identifying where invalid data enters the system, or finding root causes of cascading failures.

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Post-deploy canary monitoring. Watches the live app for console errors, performance regressions, and page failures using the browse daemon. Takes periodic screenshots, compares against pre-deploy baselines, and alerts on anomalies. Use when: "monitor deploy", "canary", "post-deploy check", "watch production", "verify deploy". (gstack)

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Diagnose and fix common AEM 6.5 LTS replication issues including blocked queues, connectivity failures, and content distribution problems

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Generate and run tests for Adobe App Builder actions and UI components. Scaffolds Jest unit tests, integration tests against deployed actions, contract tests for Adobe API interactions, and React component tests using Testing Library. Provides mock helpers for State, Files, Events SDKs, @adobe/aio-lib-* clients, ExC Shell context (@adobe/exc-app), and UIX Guest SDK (@adobe/uix-guest). Use this skill whenever the user mentions testing App Builder actions, writing unit tests for Runtime actions, creating integration tests, mocking Adobe SDKs, setting up test fixtures, running aio app test, or wants to verify action behavior before deployment. Also trigger when users mention Jest configuration for App Builder, test coverage, CI test setup, React component test, Testing Library, UI test, Provider wrapper, test my page, test my form, test my table, test my component, mock shell context, mock extension context, debug test failures, or fix Jest errors.

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Reference for producing Adobe Document Authoring (DA, da.live) and Edge Delivery Services (EDS, aka aem.live/Helix) compatible content. Use whenever generating HTML for DA upload, uploading media binaries to DA, publishing to aem.live, or driving the DA admin API (auth, source PUT, preview/publish). Covers block HTML format (canonical div-class form and accepted table alternate), section structure, page/section metadata, icons, links, images, default content, document skeleton constraints, block cell content normalization, the DA Source API contract, IMS auth, media storage, supported formats, Media Bus vs Content Bus delivery, and silent-failure rules that corrupt content.

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COMPLETE BUG INVESTIGATION WORKFLOW — Combines screenshot + log reading into a full triage pipeline. USE FOR: any bug report that has both visual symptoms AND runtime errors, especially CompositePanel / ChildPanel mount failures, screen spec wiring breaks, or battle scene UI crashes. This is the master debugging workflow that orchestrates cocos-screenshot and cocos-log-reader together.

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Decompose multi-step work into a revisable subgoal plan with stable step IDs, checkpointing, and plan-ahead execution. Load when a task needs explicit planning before action, subgoal decomposition, plan checkpointing, or ReCAP-style plan-ahead execution. Also triggers on "structured plan", "plan with steps", "subgoal graph", "revise the plan", "checkpoint plan", or multi-step tasks where naive one-shot execution would be fragile. Skips trivial single-step tasks. Pairs with dynamic-routing on failure. Distinct from process-decomposer (registry/triage) and problem-to-plan (doc deliverables).

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Apply one logical code change with mandatory impact mapping, git snapshot, verification, and automatic revert on failure. Load when the user asks for a safe edit, verified change, one change at a time with rollback, or codespine-style edit loop. Also triggers on "safe change", "edit with verification", "don't break the build", "revert if tests fail", or any non-trivial code edit where blast radius matters. Always runs dependency-mapping first. Pairs with incremental-implementation for multi-slice work; this skill is one atomic verify cycle per invocation.

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