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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 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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15
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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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19
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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 and Python 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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39
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40 COBRAxy follows several analysis paths:
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41
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42 1. **RAS Enrichment Analysis**: RAS computation → MAREA → Enriched Maps
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43 2. **Flux Enrichment Analysis Simulation**: RAS computation → Model Constraints → Flux Sampling → Flux Maps
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44 3. **RAS/RPS Enrichment Analysis**: RAS + RPS computation → MAREA → Enriched Maps
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45
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46 ## Community & Support
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47
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48 - **Documentation**: Complete guides and API reference
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49 - **Discussions**: Ask questions and share experiences
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50 - **Issues**: Report bugs and request features
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51 - **Contributing**: Help improve COBRAxy
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52
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53 ## Quick Links
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54
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55 | Resource | Description |
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56 |----------|-------------|
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57 | [Installation Guide](installation.md) | Get COBRAxy running on your system |
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58 | [Galaxy Tutorial](tutorials/galaxy-setup.md) | Web-based analysis setup |
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59 | [Python Tutorial](tutorials/python-api.md) | Use COBRAxy programmatically |
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60 | [Tools Documentation](tools/) | Complete tool reference |
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61
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62 ---
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63
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64 **Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running! |
