ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

Project-agnostic guidance for AI assistants using Chronicle. Provides search-first directives, best practices, and workflow patterns across ALL Chronicle-tracked projects. Works with or without MCP server.

Manage Chronicle project development using database-tracked milestones, next steps, and roadmap visualization. Works with MCP tools (fast, structured) or CLI commands (portable). Use when planning features, tracking progress, viewing roadmap, or linking sessions to milestones. Eliminates manual DEVELOPMENT_HISTORY.md updates.

Document chunking strategies for RAG systems. Use when implementing document processing pipelines to determine optimal chunking approaches based on document type and retrieval requirements.

Implement optimal chunking strategies in RAG systems and document processing pipelines. Use when building retrieval-augmented generation systems, vector databases, or processing large documents that require breaking into semantically meaningful segments for embeddings and search.

ci-cd-automation

Check CI/CD workflow status and troubleshoot failing checks in GitHub Actions

Monitor Nx Cloud CI pipeline and handle self-healing fixes automatically. Checks for Nx Cloud connection before starting.

Expert-level CI/CD with GitHub Actions, Jenkins, deployment pipelines, and automation

CI/CD pipeline guide covering GitHub Actions, Lefthook hooks, Dependabot, and deployment scripts. Use when asking about workflows, automation, or deployment.

Helps understand and write EAS workflow YAML files for Expo projects. Use this skill when the user asks about CI/CD or workflows in an Expo or EAS context, mentions .eas/workflows/, or wants help with EAS build pipelines or deployment automation.

Code search and intelligence using CIDX. Use when searching codebases, finding implementations, tracing call graphs, analyzing dependencies, or searching git history. Preferred over grep/find for all code exploration.

Guidance for building digital logic circuits that compute composite functions like Fibonacci of integer square root. This skill applies when implementing combinational and sequential logic in gate-level simulators, particularly when combining algorithms (like isqrt and Fibonacci) under resource constraints (gate counts, simulation steps). Use for circuit synthesis, HDL-style logic design, or gate-level algorithm implementation tasks.

Extract and validate citations with Jaccard overlap calculation. Ensures all claims have verifiable source evidence with ≥0.7 alignment threshold.

Document citations and RAG (Retrieval-Augmented Generation) patterns for Claude. Activate for source attribution, document grounding, citation extraction, and contextual retrieval.

Extract structured claims, predictions, hints, and opinions from AI research content. Use when processing tweets, blog posts, substacks, or other content from AI researchers to identify substantive assertions about AI capabilities, limitations, and progress.

Extract claims from text and map their logical relationships into structured argument networks.

Pre-ingestion verification for epistemic quality in RAG systems with 9-point verification and Two-Round HITL workflow

Build binary and multiclass classification models using logistic regression, decision trees, and ensemble methods for categorical prediction and classification

Claude in Chrome - browser automation via the official Anthropic extension. Control your logged-in Chrome browser, automate workflows, fill forms, extract data, and run scheduled tasks.

Claude Code stores its configuration and data in `~/.claude/`. This skill documents the complete structure.

Expert guide for building Claude Code hooks using the claude-hooks-sdk npm package. Use when implementing TypeScript hooks with HookManager, Logger, transforms, context tracking, or troubleshooting SDK features.

Handle photo uploads, analysis, and processing in Claude Code. This skill should be used when users want to upload images, analyze screenshots, process photos, or work with visual content in Claude Code conversations.

Anthropic 風格的專業計畫管理 Skill - 自然語言驅動、預設並行、全自動 GitHub 整合

Quick restart to reload configuration changes (skills, settings, hooks, MCP services). Use PROACTIVELY after modifying .claude/ files. Preserves conversation history.

Create comprehensive Product Requirements Documents through strategic questioning. Use when planning a new feature or project that needs clear requirements.

Best practices for implementing Clean Architecture in Remix/TypeScript apps. Covers Service Layer, Repository Pattern, and Dependency Injection.

Organize files on my desktop into tidy folders (approval required for moves)

Write clean, efficient TypeScript code that follows common best practices

Remove temporary artifacts

Expert on Shelby CLI tool for command-line blob storage operations. Helps with shelby commands, uploads, downloads, account management, context configuration, faucet operations, and CLI troubleshooting. Triggers on keywords shelby cli, shelby upload, shelby download, shelby init, shelby account, shelby context, @shelby-protocol/cli, CLI installation, shelby command.

Essential CLI tools and shell productivity patterns for efficient terminal workflows

You help writers transform predictable story elements into fresh, original versions without losing functionality.

Use when syncing data FROM relational databases (PostgreSQL, MySQL, MongoDB) TO ClickHouse. Covers change data capture using Debezium, Airbyte, or custom triggers. Includes handling schema evolution, DELETE operations, and maintaining consistency. NOT for message queues (see clickhouse-streaming) or query optimization (see clickhouse-patterns).

Implement type-safe client-server data flows in Next.js applications using Supabase, TanStack Query, React Hook Form, and Zod validation. Use when building CRUD features, handling forms with validation, implementing file uploads, or creating server actions with authentication and authorization. Essential for pages requiring data mutations with proper loading states, error handling, and query cache management.

---name: clinical-nlp-extractor

End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.

Microsoft 365 / Outlook CLI for calendar and email. Use when managing Outlook calendar (view, create, update, delete events, find meeting times, respond to invitations), sending/reading emails, or searching for people/rooms in the organization.

HTTP client for Clojure and Babashka built on java.net.http. Use when making HTTP requests, working with REST APIs, downloading files, or needing WebSocket support in Babashka or Clojure.

core.async.flow provides a declarative framework for building process flows with strict separation of application logic from topology, execution, and lifecycle management. Use when building multi-process systems, data pipelines, or when you need coordinated lifecycle management and error handling across communicating processes.

Async programming with channels, go blocks, and CSP in Clojure. Use when working with async operations, channel communication, pub/sub patterns, concurrent pipelines, or CSP-style coordination.

Shared utilities for faber-cloud plugin - configuration loading, pattern resolution, auto-discovery

AWS, GCP, Azure data platforms, infrastructure as code, and cloud-native data solutions

Cloud storage integration with signed URLs, visibility control, multi-tenant path conventions, and presigned uploads for direct client uploads.

Upload promo videos and content to Cloudflare R2 or AWS S3

Event-driven workflow automation in Flow Nexus cloud. Use for creating, executing, and managing complex automated workflows with message queue processing and intelligent agent coordination.

Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.

cloudflare-dns-operations

Comprehensive guide for managing Cloudflare DNS with Azure integration. Use when configuring Cloudflare as authoritative DNS provider for Azure-hosted applications, managing DNS records via API, setting up API tokens, configuring proxy settings, troubleshooting DNS issues, implementing DNS security best practices, or integrating External-DNS with Cloudflare for Kubernetes workloads.

Comprehensive Cloudflare account management for deploying Workers, KV Storage, R2, Pages, DNS, and Routes. Use when deploying cloudflare services, managing worker containers, configuring KV/R2 storage, or setting up DNS/routing. Requires CLOUDFLARE_API_KEY in .env and Bun runtime with dependencies installed.