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1 # COBRAxy Documentation
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2
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3 > A Python-based command-line suite for metabolic flux analysis and visualization, with Galaxy integration.
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5 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.
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6
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7 ## Overview
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8
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9 COBRAxy enables constraint-based modeling and sampling techniques, allowing users to compute metabolic
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10 flux distributions for multiple biological samples. The tool also enables the integration of medium
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11 composition information to refine flux predictions. Additionally, COBRAxy provides a user-friendly interface
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12 for visualizing significant flux differences between populations on an enriched metabolic map. This
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13 extension provides a comprehensive and accessible framework for advanced metabolic analysis, enabling
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14 researchers without extensive programming expertise to explore complex metabolic processes
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16 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.
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17
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18 ## Key Features
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20 - **Galaxy Tools** - Web-based analysis with intuitive interface
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21 - **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data
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22 - **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance
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23 - **Flux computation** - Compute metabolic flux distributions using different optimization or sampling algorithms
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24 - **Statistical Analysis** - Perform statistically significant flux differences between groups of samples and report on an enriched metabolic map
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25 - **Built-in Models** - Ready-to-use models including ENGRO2 and Recon3D
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26
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27 ## Quick Navigation
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28
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29 ### [Installation](installation.md)
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30 Install COBRAxy and get it running on your system
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31
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32 ### [Tutorials](tutorials/)
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33 Step-by-step guides for Galaxy usage
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34
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35 ### [Tools Documentation](tools/)
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36 Complete reference for all COBRAxy tools
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37
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38 ## Data Flow
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40 COBRAxy supports three main analysis workflows:
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41
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42 1. **RAS-based Enrichment Analysis**:
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43 Gene Expression → RAS Generation → MAREA → Enriched Pathway Maps
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45 2. **Flux Sampling Analysis**:
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46 Gene Expression → RAS Generation → RAS to Bounds → Flux Simulation → Flux to Map → Flux-enriched Maps
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47
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48 3. **RAS+RPS Combined Enrichment**:
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49 Gene Expression + Metabolite Data → RAS + RPS Generation → MAREA → Multi-omics Enriched Maps
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50
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51 ## Community & Support
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52
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53 - **Documentation**: Complete guides and references
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54 - **Issues**: Report bugs and request features on [GitHub](https://github.com/CompBtBs/COBRAxy/issues)
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55 - **Contributing**: Help improve COBRAxy
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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! |
