「binding」の検索結果

Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

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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 filter catalogs. Use when filtering compounds by pharmacophore features, functional groups, scaffold matches, or screening for assay-interference / structural alerts.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

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Recommend runtime and V2 scene management: run recommendation requests, manage recommend scenes and rules, and verify the deployed recommendation path.

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Build serverless applications on Azure Functions. Configure triggers, bindings, and deployment. Use when implementing serverless workloads on Azure.

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Inspect and safely edit the Claude Code and Codex configuration surfaces exposed by CCAM. Use when auditing skills, agents, commands, plugins, marketplaces, MCP servers, hooks, settings, memory, keybindings, profiles, rules, or instruction files, and when a backup-backed allowlisted edit is required.

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Scaffold Hono API routes for Cloudflare Workers. Produces route files, middleware, typed bindings, Zod validation, error handling, and API_ENDPOINTS.md documentation. Use after a project is set up with cloudflare-worker-builder or vite-flare-starter, when you need to add API routes, create endpoints, or generate API documentation.

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Native Vulkan XIR-to-SPIR-V codegen, legalization, validation, bindings, control flow, and target features.

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State machine-based vector animation with runtime interactivity and web integration. Use this skill when creating interactive animations, state-driven UI, animated components with logic, or designer-created animations with runtime control. Triggers on tasks involving Rive, state machines, interactive vector animations, animation with input handling, ViewModel data binding, or React Rive integration. Alternative to Lottie for animations requiring state machines and two-way interactivity.

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Step-by-step workflow for creating complete Power BI reports from scratch using pbir CLI. Covers model discovery, report creation, page layout, theme setup, visual placement, field binding, filtering, formatting, validation, and publishing. Automatically invoke when the user asks to "create a new report", "build a report from scratch", "make a dashboard", "set up a report with KPIs", "create an executive dashboard", "add pages and visuals to a new report".

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Use when building or fixing game UI in Godot 4.7: main menu, settings screen, HUD (health bar, ammo, minimap frame), Control layout, containers, anchors, themes in code, 'UI scales wrong on phones', 'text too small on 4K', notch or safe area, stretch mode and aspect, gamepad or keyboard menu navigation, focus lost, input rebinding screen, localization (CSV, PO, tr_n plurals, Arabic RTL, CJK fonts, pseudolocalization), screen reader accessibility, UI scale slider, or clicks not reaching the game.

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Use when structuring Unity 6.3 C# code: ScriptableObject data vs runtime state, events and services, inventory, health, save and load, Input System actions and key rebinding, async with Awaitable, assembly definitions, Enter Play Mode and domain reload, .meta files, Git, Smart Merge and LFS. Also when 'my save works in the Editor but not in the build', statics keep values on the second Play, events fire twice or never, an await runs after its object died, rebinds are lost on relaunch, a renamed class loses its data, a scene merge breaks.

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Use when structuring Godot 4.7 game code: folders, scenes and nodes, signals or an event bus autoload, custom Resources for item data, components (health, hitbox, hurtbox), an inventory, save and load, InputMap and key rebinding for keyboard, mouse and gamepad, GDScript static typing and style, or GDScript vs C#; or when code is spaghetti, a folder scan breaks in the export, a save loads wrong, the gamepad does nothing, or @onready is null.

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EU NIS2 Directive (Directive (EU) 2022/2555) compliance advisor for essential and important entities: entity classification, Art. 21 risk management measures, Art. 23 incident reporting timelines (24h/72h/1 month), Art. 20 governance obligations, supply chain security (Art. 21(2)(d); coordinated risk assessments Art. 22), gap assessments, policy drafting, ISO 27001 alignment, and penalty exposure analysis. Also covers Commission Implementing Regulation (EU) 2024/2690, the technical/methodological sub-requirements for Art. 21(2) and the significant-incident thresholds binding on DNS/cloud/data-centre/MSP/MSSP/trust-service and other digital entities. Use for NIS2 readiness, transposition questions, ENISA technical implementation guidance, significant-incident thresholds, supervisory differences between essential and important entities, and cross-border coordination.

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Query JASPAR transcription factor binding profile database

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Create, inspect, and safely update project-scoped ReachAI Agents; edit and publish Supervisor config drafts; discover published bindable Skills; and attach or detach exact Skill versions through the Agent AI Coding REST API. Use when an AI coding tool is asked to add an Agent, configure its model or prompt, bind a Skill, remove a Skill binding, or attach a published Workflow as a Tool.

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Reviews or drafts the agreement that pays an employee to settle their claims — and flags the statutory conditions that decide whether it actually binds them. Works under s.203 ERA 1996 for England & Wales. Flags apparent s.203 condition gaps for a solicitor to confirm (writing, specific complaints, independent adviser, identification, insurance, statement of conditions), drafts the substantive terms (sum, tax characterisation, confidentiality, references, restrictive covenants, indemnities), and surfaces enforceability risks. Does not rule on validity and is not legal advice. Use when the user says 'review this settlement agreement', 'draft a settlement agreement', 'compromise agreement' (old term), or asks whether an agreement is binding.

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