「enhance」の検索結果

Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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Designs donor/repair templates for precise CRISPR knock-ins -- choosing the format (ssODN, long-ssDNA/Easi-CRISPR, dsDNA/plasmid, AAV6), sizing homology arms, placing the cut within ~10 bp of the edit, and adding a mandatory codon-checked blocking (PAM/seed) mutation so the edited allele is not re-cut. Frames the HDR-vs-NHEJ-vs-MMEJ pathway competition, the MMEJ (PITCh) and homology-independent (HITI/HMEJ) alternatives for post-mitotic cells, ssODN strand/asymmetry choice, phosphorothioate end-protection, and ranked HDR enhancers. Use when designing a donor for a point mutation, epitope/fluorophore tag, allele replacement, or knock-in, or when HDR efficiency is low. Guide design and base/prime editing are separate skills.

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Infer transcription factor regulons from single-cell RNA-seq with pySCENIC by combining GRNBoost2 co-expression, cisTarget motif-enrichment pruning, and AUCell per-cell activity scoring. Covers the motif-pruning-as-directionality principle, regulon specificity scoring, run-to-run stability, and database/species matching. Use when identifying TF regulons, scoring TF activity per cell, finding master regulators of cell identity, or comparing regulon activity across conditions. For enhancer-driven multiomic GRNs see multiomics-grn; for bulk inference and VIPER protein-activity see grn-inference.

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Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021), in4mer 4-guide-array Cas12a (Esmaeili Anvar N et al 2024 Nat Commun 15:3577) and the Inzolia paralog-pair library, paralog-buffering detection (Dede 2020 Genome Biol; Thompson 2021 Cell Reports 36:109597), genetic-interaction (GI) scoring as observed_double_LFC minus expected_additive_double_LFC, synthetic-lethal and synthetic-rescue interaction interpretation, the half-of-essentiality buffered by paralogs phenomenon, multiplex screen statistical analysis with MAGeCK MLE interaction terms, and the relationship to single-cell combinatorial Perturb-seq. Use when designing a paralog or pathway-pair screen, choosing between paired-Cas9 (Big Papi) and Cas12a multiplex (Inzolia), interpreting genetic interaction scores, identifying synthetic-lethal targets for drug development, or scaling beyond single-gene CRISPR screens.

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Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Adding a file type or upgrading any of its capability slots in the files feature (preview, edit, thumbnail, grid card, info, share, versions, conversion, diff, rail panel). Use when supporting a new extension or MIME type, building a previewer, touching FILE_TYPES, PreviewKind, FilePreview.tsx, EDITABLE_KINDS, or surfaces/single-file/, or working the FILE_SURFACES.md wishlist.

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Review a feature and enhance it with purposeful animations, micro-interactions, and motion effects that improve usability and delight. Use when the user mentions adding animation, transitions, micro-interactions, motion design, hover effects, or making the UI feel more alive.

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Analyze raw prompts, identify intent and gaps, match ECC components (skills/commands/agents/hooks), and output a ready-to-paste optimized prompt. Advisory role only — never executes the task itself. TRIGGER when: user says "optimize prompt", "improve my prompt", "how to write a prompt for", "help me prompt", "rewrite this prompt", or explicitly asks to enhance prompt quality. Also triggers on Chinese equivalents: "优化prompt", "改进prompt", "怎么写prompt", "帮我优化这个指令". DO NOT TRIGGER when: user wants the task executed directly, or says "just do it" / "直接做". DO NOT TRIGGER when user says "优化代码", "优化性能", "optimize performance", "optimize this code" — those are refactoring/performance tasks, not prompt optimization.

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Review a feature and enhance it with purposeful animations, micro-interactions, and motion effects that improve usability and delight. Use when the user mentions adding animation, transitions, micro-interactions, motion design, hover effects, or making the UI feel more alive.

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MCP server optimization and transport layer enhancement for claude-flow v3. Implements connection pooling, load balancing, tool registry optimization, and performance monitoring for sub-100ms response times.

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Automated coordination, formatting, and learning from Claude Code operations using intelligent hooks with MCP integration. Includes pre/post task hooks, session management, Git integration, memory coordination, and neural pattern training for enhanced development workflows.

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Improves the quality of images, especially screenshots, by enhancing resolution, sharpness, and clarity. Perfect for preparing images for presentations, documentation, or social media posts.

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Diagnose and improve humor using systems thinking. Use when jokes fall flat, when humor feels forced, when punchlines don't land, or when you want to systematically enhance comedic writing. Treats jokes as engineerable connection systems.

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UI/UX design intelligence for web and mobile. Includes 50+ styles, 161 color palettes, 57 font pairings, 161 product types, 99 UX guidelines, and 25 chart types across 10 stacks (React, Next.js, Vue, Svelte, SwiftUI, React Native, Flutter, Tailwind, shadcn/ui, and HTML/CSS). Actions: plan, build, create, design, implement, review, fix, improve, optimize, enhance, refactor, and check UI/UX code. Projects: website, landing page, dashboard, admin panel, e-commerce, SaaS, portfolio, blog, and mobile app. Elements: button, modal, navbar, sidebar, card, table, form, and chart. Styles: glassmorphism, claymorphism, minimalism, brutalism, neumorphism, bento grid, dark mode, responsive, skeuomorphism, and flat design. Topics: color systems, accessibility, animation, layout, typography, font pairing, spacing, interaction states, shadow, and gradient.

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Optimizes Pine Script for performance, user experience, and visual appeal on TradingView. Use when improving script speed, reducing load time, enhancing UI, organizing inputs, improving colors and visuals, or making scripts more user-friendly. Triggers on "optimize", "improve", "faster", "better UX", "clean up", or enhancement requests.

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Generate ASCII art diagrams using PlantUML text mode. Use when user asks to create ASCII diagrams, text-based diagrams, terminal-friendly diagrams, or mentions plantuml ascii, text diagram, ascii art diagram. Supports: Converting PlantUML diagrams to ASCII art, Creating sequence diagrams, class diagrams, flowcharts in ASCII format, Generating Unicode-enhanced ASCII art with -utxt flag

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UI/UX design intelligence. 50 styles, 21 palettes, 50 font pairings, 20 charts, 9 stacks (React, Next.js, Vue, Svelte, SwiftUI, React Native, Flutter, Tailwind, shadcn/ui). Actions: plan, build, create, design, implement, review, fix, improve, optimize, enhance, refactor, check UI/UX code. Projects: website, landing page, dashboard, admin panel, e-commerce, SaaS, portfolio, blog, mobile app, .html, .tsx, .vue, .svelte. Elements: button, modal, navbar, sidebar, card, table, form, chart. Styles: glassmorphism, claymorphism, minimalism, brutalism, neumorphism, bento grid, dark mode, responsive, skeuomorphism, flat design. Topics: color palette, accessibility, animation, layout, typography, font pairing, spacing, hover, shadow, gradient. Integrations: shadcn/ui MCP for component search and examples.

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You are a PR optimization expert specializing in creating high-quality pull requests that facilitate efficient code reviews. Generate comprehensive PR descriptions, automate review processes, and ensure PRs follow best practices for clarity, size, and reviewability.

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Implement Microsoft's Enhanced Security Admin Environment (ESAE) tiered administration model for Active Directory. Covers Tier 0/1/2 separation, privileged access workstations (PAWs), administrative f

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Code-review quality gate and test-enhancement rubric. Use when ROSE needs sharper review output contracts, severity and risk prioritization, evidence anchors, negative review cases, fixture or golden-output drift guidance, or a Chinese review report profile; do not use as a duplicate code-review agent or final PASS authority.

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Precision Financial Insights - Analyze stocks, companies, and market sentiment using authoritative data. Powered by Yahoo Finance and enhanced with intelligent news synthesis by we-crafted.com/agents/financial-market-analysis - Buy CRAFTED_API_KEY in our website to start using

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