「three」の検索結果

Evaluates genome assembly quality across the three orthogonal axes - contiguity (QUAST auN/NG50/NGx, not bare N50), completeness (BUSCO/compleasm gene-space plus Merqury k-mer completeness), and correctness (reference-free Merqury QV, Inspector/CRAQ structural errors, asmgene false-duplication/collapse). Covers why N50 is the most-gamed metric, why QV measured on the polishing reads is circular, distinguishing uncollapsed haplotigs from real WGD, and the EBP/VGP 6.C.Q40 standard. Use when judging whether an assembly is good enough to annotate or publish, comparing assemblers, diagnosing a fragmented or duplicated assembly, or assessing a phased diploid assembly.

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Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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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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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Trigger when: (1) User mentions "manim" or "Manim Community" or "ManimCE", (2) Code contains `from manim import *`, (3) User runs `manim` CLI commands, (4) Working with Scene, MathTex, Create(), or ManimCE-specific classes. Best practices for Manim Community Edition - the community-maintained Python animation engine. Covers Scene structure, animations, LaTeX/MathTex, 3D with ThreeDScene, camera control, styling, and CLI usage. NOT for ManimGL/3b1b version (which uses `manimlib` imports and `manimgl` CLI).

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Plan, build and quality-check a premium short commercial for a real business (roofing, property, ecommerce, B2B software) using AI-generated footage, code-built motion (HTML/GSAP), selective Three.js and an independent-critic "Gauntlet" loop. Use when asked to make a launch-style / SaaS-style video, business ad, explainer, sample reel or pitch video, or to review and improve one. Encodes motion principles distilled from 28 professional launch films, a quality bar, audio rules and a business-offer playbook.

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Deep research and discovery before building something new. Explores local projects for reusable code, researches competitors, reads forums and reviews, analyses plugin ecosystems, investigates technical options, and produces a comprehensive research brief. Three depths: focused (30 min), wide (1-2 hours), deep (3-6 hours). Triggers: 'research this', 'discovery', 'explore the space', 'what should I build', 'competitive analysis', 'before I start building', 'research before coding'. Not for cited fact-checking research reports (a separate harness does those); this is pre-build product discovery.

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Modern web design trends, principles, and implementation patterns for 2024-2025. Use this skill when designing websites, creating interactive experiences, implementing design systems, ensuring accessibility, or building performance-first interfaces. Triggers on tasks involving modern design trends, micro-interactions, scrollytelling, bold minimalism, cursor UX, glassmorphism, accessibility compliance, performance optimization, or design system architecture. References animation skills (GSAP, Framer Motion, React Spring), 3D skills (Three.js, R3F, Babylon.js), and component libraries for implementation guidance.

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Lightweight WebGL/WebGPU game engine with entity-component architecture and visual editor integration. Use this skill when building browser-based games, interactive 3D applications, or performance-critical web experiences. Triggers on tasks involving PlayCanvas, entity-component systems, game engine development, WebGL games, 3D browser applications, editor-first workflows, or real-time 3D rendering. Alternative to Three.js with game-specific features and integrated development environment.

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Comprehensive skill for Babylon.js 3D web rendering engine. Use this skill when building real-time 3D experiences, browser-based games, interactive visualizations, or immersive web applications. Triggers on tasks involving Babylon.js, 3D scenes, WebGL/WebGPU rendering, entity-component systems, physics simulations, PBR materials, shadow mapping, or 3D model loading. Alternative to Three.js with built-in editor integration and game engine features.

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Comprehensive skill for GSAP (GreenSock Animation Platform) and ScrollTrigger plugin. Use this skill when creating web animations, scroll-driven experiences, timelines, tweens, scroll-triggered animations, pinning, scrubbing, parallax effects, or animating DOM elements, SVG, Canvas, WebGL, or Three.js. Triggers on tasks involving GSAP, ScrollTrigger, smooth animations, scroll effects, or animation sequencing.

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Browser-based 3D design tool with visual editor, animation, and web export. Use this skill when creating 3D scenes without code, designing interactive web experiences, prototyping 3D UI, exporting to React/web, or building designer-friendly 3D content. Triggers on tasks involving Spline, no-code 3D, visual 3D editor, 3D animation, state-based interactions, React Spline integration, or scene export. Alternative to Three.js for designers who prefer visual tools over code.

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Declarative web framework for building browser-based 3D, VR, and AR experiences using HTML and entity-component architecture. Use this skill when creating WebXR applications, VR experiences, AR experiences, 360-degree media viewers, or immersive web content with minimal JavaScript. Triggers on tasks involving A-Frame, WebXR, VR development, AR development, entity-component-system, declarative 3D, or HTML-based 3D scenes. Built on Three.js with accessible HTML-first approach.

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Deploy the dispatcher PCF for a third-party `.ppmplugin` control to a Power Platform environment via `pac pcf push`. The dispatcher PCF is the Studio-side control that dispatches the composite key `<name>/<receiver>` over the wrap shell's `SendMessagePlugin` bridge to the control's native module. Verifies deploy prereqs (Node.js 20+ with npm, .NET SDK, and active `pac auth`), then three confirmation gates — publisher prefix (2–8 chars; defaults to `pamext` or the last-used value from `.extension-state.md`), version bump (patch / minor / major / no-bump), target environment URL (from `pac org who`). Builds the PCF if needed, then pushes. Decoupled from /generate-pcf-companion so the engineer can scaffold and customize locally, then deploy when ready. Updates `.extension-state.md` with deployment history (timestamp, env URL, version, prefix used).

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Use when lighting, rendering or compositing in Blender: light a character, product or hero shot, interior at dusk or night, three-point or motivated lighting, sun and sky, HDRI, EEVEE vs Cycles settings, light leaks or noise, flat or muddy renders, subject not standing out, AgX/ACES color management, render passes, EXR, light groups, bloom and vignette in the 5.x compositor, rule of thirds and value checks, toon/NPR looks, or judging a render like a lighter.

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Use when generating or editing images with Grok Imagine models on Scenario via MCP: text-to-image, instruction editing with up to three reference images, posters, packaging, ads, or infographics with exact in-image text, photoreal shots from camera and lighting cues, extended aspect ratios up to 20:9 and 9:20, quality and resolution tiers, or batches of variations. Keywords: Grok Imagine Image 2.0, Image Quality, xAI, Aurora, Grok, txt2img, img2img, typography, 2K.

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Use when turning a song into a kinetic-typography or motion-design music video, lyric video, visualizer or K-pop style MV with Scenario, landscape or vertical 9:16 for TikTok, Reels and Shorts: a generated subject sheet, style frames and footage, plus a deterministic JavaScript/three.js engine for lyric type, mattes and tracked graphics timed to sung onsets. Also for revising, recutting or cutting teasers from such a video.

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Choose up to three immediate priorities from competing initiatives. Use when everything is urgent and the customer needs a defensible order with explicit deferrals.

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Run QA testing on a page, feature, or full site at one of three depth tiers (smoke, standard, full). Use this skill whenever the user asks to QA a page or site, run a smoke test after a deploy, verify a page before launch, or run a regression sweep. Triggers on QA, QA sweep, smoke test, regression test, post-deploy check, pre-launch check, verify the deploy, test this page, does the page render, broken link, 404, image not loading. Also triggers proactively after a deploy or a new page launch where verification matters. Covers accessibility, performance, and SEO at the surface-signal level only: deep audits belong to `accessibility-audit`, `performance-optimization`, and `seo-technical`, and code-level debugging to `code-review-web`.

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Expert SWIFT Customer Security Programme (CSP) advisor covering the Customer Security Controls Framework (CSCF v2026). Use this skill whenever a user asks about SWIFT CSP, CSCF controls, SWIFT security attestation, KYC-SA portal, SWIFT architecture types (A1/A2/A3/A4/B), mandatory vs advisory controls, independent assessment, SWIFT secure zone, secure flow zone, MFA for operators, SWIFT messaging security, payment fraud prevention on SWIFT, gap analysis for CSCF, or compliance with SWIFT's 32 controls (26 mandatory, 6 advisory in v2026) across the three objectives: Secure Your Environment, Know and Limit Access, Detect and Respond. Control 2.4 (Back-Office Data Flow Security) is now mandatory in v2026. v2026 attestation window is July 1– December 31, 2026. Trigger for any SWIFT CSP or CSCF compliance question.

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Multi-AI second opinion via OpenAI Codex CLI. Three modes: Review (pass/fail gate), Challenge (adversarial edge-case finder), Consult (freeform with session continuity). Read-only with streaming output and thinking traces. Cross-model analysis when review has already run.

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。