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scikit-bio
This skill provides access to scikit-bio, a Python library for biological data analysis. It handles sequence manipulation, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), statistical tests (PERMANOVA), and common file formats (FASTA, Newick, BIOM). The documentation includes specific code patterns for common bioinformatics tasks and troubleshooting guidance.
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
pydeseq2
This skill enables differential gene expression analysis in Python using the PyDESeq2 library. It provides workflows for loading RNA-seq count data, specifying experimental designs, running statistical tests, and generating results with multiple testing correction. The documentation includes troubleshooting for common errors like design matrix issues and memory management tips.
flowio
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
semgrep-rule-creator
Create custom Semgrep rules for detecting bug patterns and security vulnerabilities. This skill should be used when the user explicitly asks to "create a Semgrep rule", "write a Semgrep rule", "make a Semgrep rule", "build a Semgrep rule", or requests detection of a specific bug pattern, vulnerability, or insecure code pattern using Semgrep.
writing-hashql-jexpr
This skill provides detailed guidance for writing HashQL J-Expr, a JSON-based query syntax. It covers expression types, data constructors, function calls, and common patterns with clear examples. The documentation includes syntax reference and type system details, making it useful for developers working with HashQL query files.
lambda
AWS Lambda serverless functions for event-driven compute. Use when creating functions, configuring triggers, debugging invocations, optimizing cold starts, setting up event source mappings, or managing layers.
ecs
AWS ECS container orchestration for running Docker containers. Use when deploying containerized applications, configuring task definitions, setting up services, managing clusters, or troubleshooting container issues.
cloudflare-mcp-server
Build MCP servers on Cloudflare Workers - the only platform with official remote MCP support. TypeScript-based with OAuth, Durable Objects, and WebSocket hibernation. Prevents 24 documented errors. Use when: deploying remote MCP servers, implementing OAuth, or troubleshooting URL path mismatches, McpAgent exports, CORS issues, IoContext timeouts.
google-gemini-api
Integrate Gemini API with @google/genai SDK (NOT deprecated @google/generative-ai). Text generation, multimodal (images/video/audio/PDFs), function calling, thinking mode, streaming. 1M input tokens. Prevents 14 documented errors. Use when: Gemini integration, multimodal AI, reasoning with thinking mode. Troubleshoot: SDK deprecation, model not found, context window, function calling errors, streaming corruption, safety settings, rate limits.
bunjs-architecture
Provides concrete patterns for building Bun.js TypeScript backends with layered architecture. Enforces strict separation of concerns (routes, controllers, services, repositories) and mandates camelCase naming across the stack. Includes detailed workflows for database design, API endpoints, and implementation phases.
codebase-analysis
A highly structured skill for systematic codebase analysis that implements an iterative discovery-documentation-review cycle with parallel agent delegation and clear documentation standards.
video-frames
A simple wrapper around ffmpeg to extract single frames from videos at specified timestamps. It provides basic command-line examples for getting first frames or frames at specific times, with format recommendations for different use cases.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
gget
A bioinformatics tool that provides unified access to 20+ genomic databases through CLI and Python interfaces. It handles gene lookups, sequence retrieval, BLAST searches, protein structure fetching, and expression data analysis with consistent parameter patterns.
fluidsim
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
uniprot-database
Provides direct REST API access to UniProt for protein searches, FASTA retrieval, and ID mapping. Includes Python client with search, get, map, and stream functions. Well-documented with query syntax examples and field specifications. Useful for bioinformatics workflows requiring programmatic access to protein data.
ui-design-system
UI design system toolkit for Senior UI Designer including design token generation, component documentation, responsive design calculations, and developer handoff tools. Use for creating design systems, maintaining visual consistency, and facilitating design-dev collaboration.
interpreting-culture-index
Use when interpreting Culture Index surveys, CI profiles, behavioral assessments, or personality data. Supports individual interpretation, team composition (gas/brake/glue), burnout detection, profile comparison, hiring profiles, manager coaching, interview transcript analysis for trait prediction, candidate debrief, onboarding planning, and conflict mediation. Handles PDF vision or JSON input.
artifacts-builder
Provides shell scripts to scaffold a React+TypeScript+Vite project with Tailwind CSS and 40+ shadcn/ui components, then bundle it into a single HTML file for Claude artifacts. Includes Node version detection, path alias configuration, and design guidelines to avoid common AI-generated UI patterns.
testing-hashql
Provides detailed guidance for testing HashQL compiler code using compiletest UI tests, unit tests, and insta snapshots. Covers test structure, annotation syntax, debugging failures, and updating expected outputs with --bless. Includes concrete examples for different testing scenarios and clear command references.
thought-based-reasoning
This skill provides a structured guide to Chain-of-Thought prompting and its variants for improving LLM reasoning. It includes decision matrices, prompt templates, and research-backed patterns for techniques like Zero-shot CoT, Self-Consistency, Tree of Thoughts, and ReAct. The documentation helps users select appropriate methods for different reasoning tasks.
Gathering Requirements
This skill provides a structured methodology for clarifying user requirements before implementation. It guides through request classification, system investigation, targeted questioning, assumption resolution, and specification creation. The workflow helps prevent misunderstandings by systematically uncovering edge cases, performance expectations, and integration points.
Writing Documentation for LLMs
Provides concrete guidelines for writing documentation optimized for LLM consumption. Focuses on token efficiency, progressive disclosure, and specific patterns like 'What + When' descriptions. Includes anti-patterns and practical examples for API docs and code documentation.