umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
treatment-plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
workflow-patterns
TDD task implementation patterns - red-green-refactor cycle, phase checkpoints, git commits, and verification protocols for quality assurance.
torchdrug
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
yara-authoring
YARA-X detection rule authoring with expert judgment, linting, atom analysis, and best practices. Teaches how to think like an expert YARA author for malware detection, threat hunting, and indicator-of-compromise identification using YARA-X (the Rust-based successor to legacy YARA).
writing-skills
TDD applied to documentation - create production-ready skills. Use when authoring new skills. Includes writing style guidelines for clear prose.
workflow-creator
Creates multi-agent orchestration workflows for complex tasks. Handles enterprise workflows, operational procedures, and custom orchestration patterns. Use when user needs to automate multi-phase processes with agent coordination.
windows-terminal
Spawn and manage Windows Terminal (wt.exe) windows and tabs from Node.js scripts and Claude Code hooks, with App Execution Alias resolution, correct CLI flags, and anti-patterns to avoid
websocket-engineer
Expert WebSocket and real-time communication engineering — WebSocket protocol (RFC 6455), ws/Socket.IO server implementation, authentication, heartbeat/reconnection, horizontal scaling with Redis pub/sub, Server-Sent Events (SSE), WebRTC signaling, and observability. Use for chat, live dashboards, multiplayer, collaborative editing, and event-driven real-time systems.
webmcp-browser-tools
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state-management-expert
State management expert including MobX, Redux, Zustand, and reactive patterns
webapp-testing
Test local web applications using Playwright with Python. Verify frontend functionality, debug UI behavior, capture screenshots, and view browser console logs. Supports static HTML files, dynamic webapps with running servers, and automated test generation.
web3-expert
Web3 and blockchain expert including Solidity, Ethereum, and smart contracts
web-perf
Structured 5-phase web performance audit workflow with Core Web Vitals thresholds and actionable optimization recommendations. Use when auditing website performance, diagnosing slow page loads, optimizing Core Web Vitals scores, or reviewing frontend performance patterns. Covers Webpack, Vite, Next.js, and Nuxt optimization.
web-design-guidelines-vercel
Review UI code for Web Interface Guidelines compliance. Use when asked to "review my UI", "check accessibility", "audit design", "review UX", or "check my site against best practices".
wave-executor
Fresh-process orchestration for EPIC-tier batch pipelines. Spawns a new Bun process per wave via the Claude Agent SDK, preventing GC-related crashes in long-running sessions.
spec-to-code-compliance
Verify that implementation code faithfully implements its specification — checks function contracts, API contracts, and protocol compliance against source specifications
spec-init
Unified skill that guides spec creation through structured, interactive process.
spec-gathering
Requirements gathering workflow for specification creation. Use when starting a new feature, task, or project that needs structured requirements.
sparc-methodology
SPARC (Specification, Pseudocode, Architecture, Refinement, Completion) comprehensive development methodology with multi-agent orchestration
smart-debug
AI-assisted debugging specialist with deep knowledge of modern debugging tools, observability platforms, and automated root cause analysis. Implements Cursor Debug Mode methodology — structured hypothesis ranking, targeted code instrumentation, human-in-the-loop reproduction gate, log-confirmed root cause, and mandatory cleanup.
slack-notifications
Slack messaging, channels, and notifications - send messages, manage channels, interact with users, upload files, and add reactions. Use for team communication, incident notifications, and workflow alerts.
workflow-updater
Research-backed workflow to refresh existing workflow files with phase-gate regression checks, idempotency validation, and ecosystem alignment.
slack-expert
Expert-level Slack platform development using Bolt SDK — build Slack apps with slash commands, interactive components (buttons, modals, shortcuts), home tabs, event subscriptions, workflows, Socket Mode, and Block Kit. Use for building Slack bots, workflow automation, and rich interactive Slack experiences.
skill-updater
Research-backed skill refresh workflow for updating existing skills with TDD checkpoints, memory-aware integration, and EVOLVE/reflection trigger handling.
nextjs-expert
Next.js framework expert including App Router, Server Components, and API routes
nodejs-expert
Node.js backend expert including Express, NestJS, and async patterns
notification-triggers
Configurable regex-based alert system for detecting patterns in tool calls and session activity. Supports error triggers, content regex matching, token threshold triggers, and pattern detection with configurable actions.
omega-claude-cli
Shell out to Claude Code CLI to invoke a second Claude session headlessly. Useful for cross-validation, second opinions, and isolated analysis without sharing current agent context. Requires Anthropic account.
datacommons-client
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
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.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
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.
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.
lsp-navigator
Compiler-level code intelligence via native LSP — definitions, references, types, call hierarchies, and diagnostics.
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