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1 # COBRAxy Documentation
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2
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3 > A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration.
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4
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5 COBRAxy transforms gene expression and metabolite data into meaningful metabolic insights through flux sampling and interactive pathway maps.
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6
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7 ## Overview
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8
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9 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.
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10
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11 ## Key Features
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12
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13 - **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data
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14 - **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance
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15 - **Flux Sampling** - Sample metabolic flux distributions with CBS or OptGP algorithms
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16 - **Statistical Analysis** - Perform pFBA, FVA, and sensitivity analysis
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17 - **Interactive Maps** - Generate publication-ready pathway visualizations with SVG/PDF export
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18 - **Galaxy Tools** - Web-based analysis with intuitive interface
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19 - **Built-in Models** - Ready-to-use models including ENGRO2 and Recon
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20
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21 ## Quick Navigation
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22
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23 ### [Installation](installation.md)
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24 Install COBRAxy and get it running on your system
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25
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26 ### [Tutorials](tutorials/)
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27 Step-by-step guides for Galaxy and Python usage
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28
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29 ### [Tools Documentation](tools/)
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30 Complete reference for all COBRAxy tools
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31
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32 ## Data Flow
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33
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34 COBRAxy follows two parallel analysis paths:
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35
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36 1. **Enrichment Analysis**: RAS + RPS → MAREA → Enriched Maps
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37 2. **Flux Simulation**: RAS → Model Constraints → Flux Sampling → Flux Maps
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38
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39 ## Community & Support
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40
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41 - **Documentation**: Complete guides and API reference
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42 - **Discussions**: Ask questions and share experiences
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43 - **Issues**: Report bugs and request features
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44 - **Contributing**: Help improve COBRAxy
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45
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46 ## Quick Links
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47
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48 | Resource | Description |
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49 |----------|-------------|
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50 | [Installation Guide](installation.md) | Get COBRAxy running on your system |
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51 | [Galaxy Tutorial](tutorials/galaxy-setup.md) | Web-based analysis setup |
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52 | [Python Tutorial](tutorials/python-api.md) | Use COBRAxy programmatically |
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53 | [Tools Documentation](tools/) | Complete tool reference |
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54
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55 ---
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56
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57 **Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running! |
