'modes' 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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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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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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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Use this skill when an inspector requests ELD records during a roadside inspection. Covers the three required transfer methods, what data must be transmitted, and common failure modes.

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Audit a compliance-ladder design (C0-C6) and transcript-fidelity ladder (T0-T5) plus their adapter conformance fixtures — Codex, Claude Code, Cloudflare, Ollama/LM Studio, custom stdio/HTTP agents — for the two failure modes that make a C-badge or T-fidelity label a lie: the ladder disagreeing with itself across doc/schema/ui/probe surfaces, and a level being reachable by self-report because no daemon-witnessed negative probe actually tries to forge it. Use when designing or freezing a compliance ladder, wiring an adapter conformance probe suite, deciding whether a numeric C-badge or T-label is safe to ship, or investigating a self-attestation or observed-to-controlled bypass risk. NOT for auditing a cryptographic protocol or whitepaper for adversarial soundness (`redteam-review`), writing TLA+/formal invariants for a daemon monitor (`runtime-verification-for-agents`), or agent identity, successor linkage, and reputation across restarts (`agent-identity-continuity-reputation`).

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Design discovery, directories, and guilds for agent swarms at scale. Use when agents need to find each other on a shared surface: capability indices, yellow-pages directories, whois/phonebook routing, reputation-aware discovery, and guild structures that scope trust. Covers the canonical prior art (FIPA Directory Facilitator, Contract Net, Chord/DHT, DNS-SD/Consul, EigenTrust, Greif's merchant guilds) and the failure modes (read-poverty, Sybil reset, Goodhart on rank, directory staleness, cold-start). Triggers: "agents can't find each other", "who owns this file/skill", "route a question to the right agent", "capability registry", "agent reputation", "guild / federation of fleets". NOT for issuing identities, granting authority, or automatically assigning work from a directory entry.

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Discover failure modes in Coval runs, uploaded conversations or local conversation exports using scoped sampling and transcript, audio and trace evidence. Prepare human review without inventing ground truth or launching new runs.

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Scaffold recipe for a new authenticated route: SSR shell, DB-derived types, Redux hydration, view sub-pages. Use when creating a new route or page, adding a feature with a sidebar/main layout, adding view modes to a route, or feature types don't match database.types.ts.

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Fetch any URL and convert to markdown using Chrome CDP. Supports two modes - auto-capture on page load, or wait for user signal (for pages requiring login). Use when user wants to save a webpage as markdown.

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Interactive training for the GitHub Copilot CLI. Guided lessons, quizzes, scenario challenges, and a full reference covering slash commands, shortcuts, modes, agents, skills, MCP, and configuration. Say "cliexpert" to start.

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12-agent academic paper writing pipeline on Hermes Agent. 10 modes (full/plan/outline/revision/revision-coach/abstract/lit-review/format-convert/citation-check/disclosure). 6 paper types, 5 citation formats, bilingual abstracts, LaTeX/DOCX/PDF output. Uses delegate_task for each agent. Triggers: write paper, academic paper, guide my paper, parse reviews, AI disclosure, 寫論文, 學術論文, 引導我寫論文, 審查意見.

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7-agent paper review system on Hermes Agent. 6 modes (full/re-review/quick/methodology-focus/guided/calibration). 5-panel review with editorial decision, revision roadmap, and calibration metrics. Uses delegate_task for each reviewer. Triggers: review paper, peer review, manuscript review, check revisions, calibrate reviewer, 審稿, 同儕審查, 論文審查.

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Tunes GC and memory. GC modes, LOH/POH, Gen0/1/2, Span/Memory deep patterns, ArrayPool.

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Architects Blazor apps. Hosting models, render modes, routing, streaming, prerender.

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Use when building, testing or previewing site-os — the BUILD_TARGET=stable dist directory, the four verification gates (build, test, env:check, brand:check), the preview servers on :3000 and :3100, and the failure modes that look like bugs but are not.

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Static-to-EDS conversion that preserves the original design while making content authorable in Document Authoring. Two modes — page-level (overlay template with slot markers) and block-level (each section becomes an independent EDS block). Use when converting an AI-generated static HTML page (Stardust, Mobirise, Relume, Lovable, v0, Figma-derived hand-coded, etc.) into an Edge Delivery Services page. Triggers on "convert this page to EDS", "static-to-EDS overlay", "convert to EDS blocks", "next experimentation", "next run", "start run", or when a user provides a source URL and asks to make it editable in DA while keeping the original design intact. Do NOT use for canonical EDS block-rewrite migrations — that's the page-import skill.

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Creates data table patterns with filtering, sorting, pagination, row actions, column configuration, server/client rendering modes, and empty/loading states. Use when building "data tables", "list views", "admin tables", or "data grids".

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Control LG smart appliances via ThinQ API. Use when user asks about their fridge, washer, dryer, AC, or other LG appliances. Supports checking status, changing temperature, toggling modes (express, eco), and monitoring door status.

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Human-in-the-loop CAPTCHA solving with two modes: screenshot (default, zero infrastructure) and token relay (requires network access). Screenshot mode captures the page with a grid overlay, sends it to the human, and injects clicks based on their reply. Token relay mode detects CAPTCHA type + sitekey, serves the real widget on a relay page for native solving, and injects the token via CDP.

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Analyze Claude Code features and capabilities to uncover advanced usage patterns, best practices, and real-world application scenarios. Use this skill whenever the user mentions a Claude Code feature (like Streaming Tool Execution, Hooks, MCP, Skills, Subagents, Context Management, Permission Modes, etc.) and wants to know how to leverage it effectively — including advanced tips, workflow optimizations, creative use cases, and pitfalls to avoid. Also trigger when the user pastes a feature description or asks 'how to use X better in Claude Code', even without explicitly saying 'analyze'.

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