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Agents
Dynamic agent composition and management system. USE WHEN user says create custom agents, spin up custom agents, specialized agents, OR asks for agent personalities, available traits, agent voices. Handles custom agent creation, personality assignment, voice mapping, and parallel agent orchestration.
single-cell-preprocessing-with-omicverse
This skill provides step-by-step instructions for preprocessing single-cell RNA-seq data using the omicverse library. It covers QC, normalization, HVG selection, and embedding generation across CPU, mixed CPU-GPU, and GPU environments. Includes defensive checks for clustering and batch-aware HVG selection patterns.
langchain4j-spring-boot-integration
A comprehensive integration guide for LangChain4j with Spring Boot, offering practical patterns for AI-powered Java applications with good security practices and production readiness.
creating-agents-md
Use when creating agents.md files - provides plain markdown format with NO frontmatter, free-form structure, and project context guidelines for AI coding assistants
ts-agent-sdk
Generate typed TypeScript SDKs for AI agents to interact with MCP servers. Converts JSON-RPC curl commands to clean function calls. Auto-generates types, client methods, and example scripts from MCP tool definitions. Use when building MCP-enabled applications, need typed programmatic access to MCP tools, or creating reusable agent automation scripts.
smart-suggestions
This skill makes the AI assistant suggest logical next steps after completing tasks, guiding users through project phases like UI creation, logic implementation, and deployment. It provides 2-3 context-aware options based on project state and business type.
vibe-orchestrator
A master controller for Lovable-style development that immediately generates working UI from any prompt. It routes tasks to specialized sub-agents (UI builder, dev builder, design reviewer) and enforces a strict memory protocol to maintain project context across sessions. The skill prioritizes creating premium, multi-page applications with animations and realistic mock data before backend integration.
anndata
This skill provides comprehensive guidance for working with AnnData objects in Python, covering creation, I/O operations, concatenation, and integration with tools like Scanpy. It includes practical examples for single-cell genomics workflows, error handling, and common pitfalls. The documentation is detailed with clear code snippets for real-world tasks.
atlas14-spatial-variance
This skill analyzes spatial variability of NOAA Atlas 14 precipitation data within HEC-RAS model domains. It helps engineers decide if uniform rainfall assumptions are valid for rain-on-grid modeling by calculating min/max/mean statistics. It uses HTTP byte-range requests to download only needed data, reducing transfer by 99.9% compared to traditional methods.
histolab
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
building-chat-widgets
Provides patterns for building interactive chat widgets with client/server actions, entity tagging, and widget lifecycle management. Includes TypeScript/Python examples for handling button clicks, form submissions, and real-time widget updates in agent conversations.
simpy
This skill provides a Python-based discrete-event simulation framework for modeling systems with processes, queues, and shared resources. It includes templates for manufacturing, logistics, and service operations, with monitoring utilities for data collection and analysis.
gap-analysis
This skill acts as a central dispatcher for gap analysis tasks. It parses natural language queries to identify intent (security, compliance, testing), routes requests to appropriate specialized skills, aggregates their findings into a unified report, and compares results against historical data. It supports custom criteria saving and parallel execution.
single-cell-clustering-and-batch-correction-with-omicverse
This skill provides step-by-step guidance for single-cell RNA-seq analysis using omicverse. It covers data preprocessing, multiple clustering methods, batch correction techniques, and quality evaluation. The instructions include dependency checks and troubleshooting tips for common errors.
bulk-rna-seq-deconvolution-with-bulk2single
This skill enables reconstruction of single-cell profiles from bulk RNA-seq data using a beta-VAE approach. It provides step-by-step instructions for data loading, fraction estimation, model training, synthetic cell generation, and benchmarking against reference scRNA-seq atlases.
spatial-transcriptomics-tutorials-with-omicverse
This skill provides guided access to spatial transcriptomics tutorials using the omicverse Python library. It walks users through preprocessing, cell deconvolution, and downstream analysis workflows for datasets like Visium and Slide-seq. The instructions include specific code examples for tasks like cell segmentation with Cellpose and spatial integration with STAligner.
proxy-mode-reference
A comprehensive reference guide for orchestrating multi-model AI workflows through PROXY_MODE directive, enabling seamless integration of external AI models within Claude's agent system.
langchain4j-mcp-server-patterns
Comprehensive implementation guide for building MCP servers with LangChain4j, offering clear patterns for tools, resources, and prompts with enterprise-grade Spring Boot integration.
spring-data-jpa
A comprehensive and well-structured Skill for implementing Spring Data JPA persistence layers with clear examples, best practices, and coverage of essential features like auditing, pagination, and transactions.
SDK Analytics Installer
This skill provides step-by-step instructions for installing and configuring the dotCMS analytics SDK in Next.js projects. It focuses on correct usage patterns, emphasizes centralized configuration, and warns about common pitfalls like the lack of React context for the tracking hook. The guide includes concrete examples for page views, custom events, and conversions.
bulk-rna-seq-batch-correction-with-combat
This skill provides a step-by-step workflow for applying ComBat batch correction to bulk RNA-seq data using the omicverse Python package. It guides users through loading multiple datasets, merging them, running correction, exporting results, and visualizing improvements. The instructions include troubleshooting tips for common issues like gene identifier mismatches.
agentdb-learning
A comprehensive reinforcement learning toolkit for AgentDB that provides 9 different algorithms with clear documentation and practical examples for building self-learning agents.
esm
Provides access to ESM3 for generative protein design (sequence, structure, function) and ESM C for protein embeddings. Includes detailed code examples for tasks like inverse folding, structure prediction, and function annotation. Supports both local models and cloud API.
shopify
Build Shopify applications, extensions, and themes using GraphQL/REST APIs, Shopify CLI, Polaris UI components, and Liquid templating. Capabilities include app development with OAuth authentication, checkout UI extensions for customizing checkout flow, admin UI extensions for dashboard integration, POS extensions for retail, theme development with Liquid, webhook management, billing API integration, product/order/customer management. Use when building Shopify apps, implementing checkout customizations, creating admin interfaces, developing themes, integrating payment processing, managing store data via APIs, or extending Shopify functionality.