'functional' 검색 결과

Analyzes base-editing screens for variant function. Covers library design (Sanson 2020 GRACE, Hanna 2021 BRCA1/2 SNV scanning, Cuella-Martin 2021), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end, wider for ABE8e), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and reactive/PAINS/REOS/Brenk/Aldridge filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

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Guides the practical path from 'we have no design system' or 'we have a mess' to a real, functional design system. Component inventory, design token extraction, headless UI adoption (Radix, React Aria, Headless UI), migration order of operations, and the assessment-to-rollout pipeline. Activate on 'design system from scratch', 'bootstrap design system', 'no design system', 'design system migration', 'headless UI adoption', 'component audit', 'design token extraction', 'design system strategy'. NOT for building specific components once a system exists (use design-system-creator), not for generating token files/configs (use design-system-generator).

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Use when implementing features or fixing bugs with strict Test-Driven Development (TDD). Activate for coding tasks that require new functionality, refactoring, or comprehensive test coverage, especially when the user mentions TDD or Test Driven Development.

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Use when starting creative work (features, components, functionality, or behavior changes) to clarify user intent, requirements, and design before implementation.

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Add moments of joy, personality, and unexpected touches that make interfaces memorable and enjoyable to use. Elevates functional to delightful. Use when the user asks to add polish, personality, animations, micro-interactions, delight, or make an interface feel fun or memorable.

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ALWAYS use this skill when user needs ANY API functionality (AI models, image generation, video, audio, text processing, etc.). Automatically search 302.AI's 1400+ APIs and generate integration code. Use proactively whenever APIs or AI capabilities are mentioned.

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Create test versions to verify app auto-update functionality. Use when testing update flows, version migration, or validating app upgrade mechanisms. Automates version number and build number configuration for testing the auto-update system. Triggers on auto update, app upgrade, update testing, upgrade flow, version migration, test build, 9XXX version.

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コードを実装・修正・リファクタリングするすべてのタスクで使うスキル。純粋関数を中心に設計し、副作用(DB、HTTP、ファイル、時刻、乱数、ログなど)を境界へ寄せ、データ変換、エラー表現、コレクション操作、可変状態の扱いを既存コードに合う形で整理する。ユーザーが明示的に指示しなくても、言語を問わず、コードを書き始める前に発火する。設定値やドキュメントだけの変更では不要。

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Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

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Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis.

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Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities. This skill should be used when the user is looking for functionality that might exist as an installable skill.

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You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

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Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.

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Writes production-quality Pine Script v6 code following TradingView guidelines and best practices. Use when implementing indicators, strategies, or any Pine Script code. Triggers on requests to create, write, implement, or code Pine Script functionality.

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Be the COO with process design, organizational scaling, cross-functional execution, and operational excellence.

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Adds a complete blog feature to an existing Blazor WebAssembly Static Web App with Azure Functions backend and Azure File Share for markdown storage. Use when implementing blog functionality in .NET Blazor WASM projects with Azure infrastructure. Includes post listing, detail pages, markdown rendering, Azure Storage integration.

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Master enterprise-grade Scala development with functional programming, distributed systems, and big data processing. Expert in Apache Pekko, Akka, Spark, ZIO/Cats Effect, and reactive architectures. Use PROACTIVELY for Scala system design, performance optimization, or enterprise integration.

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Expert Haskell engineer specializing in advanced type systems, pure functional design, and high-reliability software. Use PROACTIVELY for type-level programming, concurrency, and architecture guidance.

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