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End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-specific UMI extraction, ENCODE STAR parameters, CLIPper or Skipper peak calling with stringent log2 FC and -log10 p thresholds, IDR rescue and self-consistency QC, and downstream motif registration with mCross or PEKA.

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Agentic and machine-to-machine payments on Stellar. Covers x402 (HTTP 402 paid APIs via OZ Channels facilitator, fee-sponsored clients) and MPP (Machine Payments Protocol) in both Charge mode (per-request SAC) and Channel mode (off-chain commits, high-frequency). Defaults to USDC (SEP-41 SAC) on `stellar:testnet`/`stellar:pubnet` (CAIP-2). Use when selling a paid API to AI agents, building an x402 client, or designing a payment-channel architecture for high-frequency agent traffic.

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Stellar standards, ecosystem, and reference. Covers SEPs (Stellar Ecosystem Proposals), CAPs (Core Advancement Proposals), and a quick map for picking the right standard for wallets, anchors, payments, deposits/withdrawals, federation, deep links, and KYC. Also bundles ecosystem references (DeFi protocols, dev tools, wallets, infra, community projects), curated documentation links, and MCP servers (live tools such as Raven). Use when you need to know which SEP applies, or want a starting point for ecosystem integrations, official docs, or live MCP tooling.

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Windows アプリ開発 (Windows App SDK / WinRT) の OS 統合 API リファレンス。 DeviceInformation, DeviceWatcher, センサー (Accelerometer, Gyrometer, Pedometer, Compass, OrientationSensor, ActivitySensor), Bluetooth LE, USB, Serial, HID, Battery, HttpClient, StreamSocket, WebSocket, BackgroundDownloader/Uploader, NetworkInformation, PointerInput, KeyboardInput, IME/TextInput, FocusManager, DragAndDrop, ResourceLoader (多言語化・地域化), Calendar, DateTimeFormatter, CurrencyFormatter, PasswordVault, OAuth2Manager, Web Account Manager (WAM) / MSAL, WebAuthenticationBroker, WindowsHello/Passkeys, Age signals, CryptographicBuffer, Clipboard, DataTransferManager, Launcher, ProtocolActivation, JumpList, TaskbarManager, SecondaryTile, StartupTask, Smart App Control, Phone Link。

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OpenAI API (developers.openai.com) の Agents SDK (Python / TypeScript)・Agents API (beta)。 Agent, Runner, handoffs, guardrails, tracing, SandboxAgent、 client.beta.agents の sessions / environments / vaults / plugins、 built-in tools（web search, file search, computer use, code interpreter, image generation）、 function tools, vector stores, MCP (Model Context Protocol) connectors, background mode, multi-agent orchestration。

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Blender Python API リファレンス。bpy / bmesh / mathutils / gpu / bpy_extras モジュール、 bpy.data / bpy.context / bpy.ops / bpy.types / bpy.props / bpy.msgbus / bpy.path コア API。 Mesh / Modifier / Geometry Nodes / Armature / Keyframe / Driver / Shape Key / NLA、 Cycles / EEVEE / Shader Nodes / Rigid Body / Cloth / Fluid / Compositor Nodes / AOV、 headless CLI レンダリング、add-on 開発、Extensions システム、MCP Server (Model Context Protocol)。

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Claude Code (code.claude.com) デプロイ・CI/CD リファレンス。 Amazon Bedrock / Google Cloud Agent Platform (Vertex AI) / Microsoft Foundry / Claude Platform on AWS、 Claude apps gateway、LLM gateway (protocol / rollout)、 GitHub Actions (claude-code-action) / GitLab CI/CD / GitHub Enterprise Server (GHES)、 Code Review (REVIEW.md・review level・@claude review always・コスト・トラブルシュート)、 ローカル /code-review、ultrareview (claude ultrareview)、 Slack (Claude Tag、旧 Claude Code in Slack、Pro/Max)、 headless mode、cloud environments、devcontainer、 self-hosted environments（runner 構成・identity 検証・本番デプロイ）。

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Analyze binaries or protocols you own (or have license to inspect) to improve security, compatibility, or incident response. Not for cracking, DRM bypass, or malware creation.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Use when building MCP (Model Context Protocol) servers in Java/Spring Boot. Covers tool registration, resource exposure, prompt templates, and production deployment using the official MCP Java SDK. Use when user mentions MCP, AI agent integration, or tool calling.

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Build production-ready Web3 applications, smart contracts, and decentralized systems. Implements DeFi protocols, NFT platforms, DAOs, and enterprise blockchain integrations.

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Built-in MCP (Model Context Protocol) client that connects to external MCP servers, discovers their tools, and registers them as native Hermes Agent tools. Supports stdio and HTTP transports with automatic reconnection, security filtering, and zero-config tool injection.

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Review or refactor an existing SKILL.md and its bundled resources — a smaller always-loaded core, conditional references, preserved behavior, lean/guided consumer profiles, and an A/B protocol to compare a candidate with the previous version. Use when a skill repeats itself, loads references on every run, triggers too broadly or misses legitimate requests, or needs its efficiency measured across models. Do NOT use for writing a new skill from scratch, refactoring application code, translating a skill verbatim, or performing the target skill's own task.

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Build Model Context Protocol (MCP) servers and tools that extend Claude's capabilities with custom functions, data sources, and integrations. Use when creating custom MCP servers, implementing tools for Claude, building integrations with external services, creating data source connectors, implementing custom functions, or extending Claude's capabilities with domain-specific tools.

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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Build production-ready Web3 applications, smart contracts, and decentralized systems. Implements DeFi protocols, NFT platforms, DAOs, and enterprise blockchain integrations.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a scRNA-seq / surface-protein / chromatin readout. Covers experimental design (direct-capture Perturb-seq Dixit 2016 vs CROP-seq 3'UTR-barcoded Datlinger 2017 vs ECCITE-seq vs Multiome), MOI for sgRNA assignment, escaper-cell filtering (Mixscape, Papalexi 2021), SCEPTRE NB GLM + permutation for low-MOI (Barry 2024 Genome Biol 25:124), the Pertpy framework, factor decomposition, genome-scale Perturb-seq (Replogle 2022 Cell, 2.5M cells), and per-perturbation single-cell DE. Use when running a single-cell CRISPR screen, choosing direct-capture vs CROP-seq architecture, filtering escaper cells, performing single-cell DE, integrating Perturb-seq with pathway analysis, scaling to GW CRISPRi via Replogle protocol, or analyzing multi-omics screens.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 7.

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