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# COBRAxy Documentation

> A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration.

COBRAxy enables the integration of transcriptomics data with COBRA-based metabolic models, offering a comprehensive framework for studying metabolism in both health and disease. With COBRAxy, users can load and enrich metabolic models by incorporating transcriptomic data and adjusting the model’s medium conditions.

## Overview

COBRAxy enables constraint-based modeling and sampling techniques, allowing users to compute metabolic
flux distributions for multiple biological samples. The tool also enables the integration of medium
composition information to refine flux predictions. Additionally, COBRAxy provides a user-friendly interface
for visualizing significant flux differences between populations on an enriched metabolic map. This
extension provides a comprehensive and accessible framework for advanced metabolic analysis, enabling
researchers without extensive programming expertise to explore complex metabolic processes

By offering an intuitive and accessible platform for multi-omics integration and metabolic analysis, COBRAxy meets the growing need for tools that help researchers explore complex metabolic processes with ease.

## Key Features

- **Galaxy Tools** - Web-based analysis with intuitive interface
- **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data
- **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance
- **Flux computation** - Compute metabolic flux distributions using different optimization or sampling algorithms
- **Statistical Analysis** - Perform statistically significant flux differences between groups of samples and report on an enriched metabolic map
- **Built-in Models** - Ready-to-use models including ENGRO2 and Recon3D

## 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 several analysis paths:

1. **RAS Enrichment Analysis**: RAS computation → MAREA → Enriched Maps
2. **Flux Enrichment Analysis Simulation**: RAS computation → Model Constraints → Flux Sampling → Flux Maps
3. **RAS/RPS Enrichment Analysis**: RAS + RPS computation → MAREA → Enriched 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 |

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**Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running!