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+# COBRAxy Documentation
+
+> A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration.
+
+COBRAxy transforms gene expression and metabolite data into meaningful metabolic insights through flux sampling and interactive pathway maps.
+
+## Overview
+
+COBRAxy provides a complete pipeline for metabolic modeling and analysis, from raw omics data to publication-ready pathway visualizations. Whether you're a researcher analyzing metabolic changes in disease, a systems biologist studying metabolic networks, or a bioinformatician building analysis pipelines, COBRAxy offers the tools you need.
+
+## Key Features
+
+- **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data
+- **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance
+- **Flux Sampling** - Sample metabolic flux distributions with CBS or OptGP algorithms  
+- **Statistical Analysis** - Perform pFBA, FVA, and sensitivity analysis
+- **Interactive Maps** - Generate publication-ready pathway visualizations with SVG/PDF export
+- **Galaxy Tools** - Web-based analysis with intuitive interface
+- **Built-in Models** - Ready-to-use models including ENGRO2 and Recon
+
+## Quick Navigation
+
+### [Installation](installation.md)
+Install COBRAxy and get it running on your system
+
+### [Tutorials](tutorials/)
+Step-by-step guides for Galaxy and Python usage
+
+### [Tools Documentation](tools/)
+Complete reference for all COBRAxy tools
+
+## Data Flow
+
+COBRAxy follows two parallel analysis paths:
+
+1. **Enrichment Analysis**: RAS + RPS → MAREA → Enriched Maps
+2. **Flux Simulation**: RAS → Model Constraints → Flux Sampling → Flux Maps
+
+## Community & Support
+
+- **Documentation**: Complete guides and API reference
+- **Discussions**: Ask questions and share experiences
+- **Issues**: Report bugs and request features
+- **Contributing**: Help improve COBRAxy
+
+## Quick Links
+
+| Resource | Description |
+|----------|-------------|
+| [Installation Guide](installation.md) | Get COBRAxy running on your system |
+| [Galaxy Tutorial](tutorials/galaxy-setup.md) | Web-based analysis setup |
+| [Python Tutorial](tutorials/python-api.md) | Use COBRAxy programmatically |
+| [Tools Documentation](tools/) | Complete tool reference |
+
+---
+
+**Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running!
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