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1 # COBRAxy Documentation 1 # COBRAxy Documentation
2 2
3 > A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration. 3 > A Python-based command-line suite for metabolic flux analysis and visualization, with Galaxy integration.
4 4
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. 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.
6 6
7 ## Overview 7 ## Overview
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9 COBRAxy enables constraint-based modeling and sampling techniques, allowing users to compute metabolic 9 COBRAxy enables constraint-based modeling and sampling techniques, allowing users to compute metabolic
10 flux distributions for multiple biological samples. The tool also enables the integration of medium 10 flux distributions for multiple biological samples. The tool also enables the integration of medium
28 28
29 ### [Installation](installation.md) 29 ### [Installation](installation.md)
30 Install COBRAxy and get it running on your system 30 Install COBRAxy and get it running on your system
31 31
32 ### [Tutorials](tutorials/) 32 ### [Tutorials](tutorials/)
33 Step-by-step guides for Galaxy and Python usage 33 Step-by-step guides for Galaxy usage
34 34
35 ### [Tools Documentation](tools/) 35 ### [Tools Documentation](tools/)
36 Complete reference for all COBRAxy tools 36 Complete reference for all COBRAxy tools
37 37
38 ## Data Flow 38 ## Data Flow
39 39
40 COBRAxy follows several analysis paths: 40 COBRAxy supports three main analysis workflows:
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42 1. **RAS Enrichment Analysis**: RAS computation → MAREA → Enriched Maps 42 1. **RAS-based Enrichment Analysis**:
43 2. **Flux Enrichment Analysis Simulation**: RAS computation → Model Constraints → Flux Sampling → Flux Maps 43 Gene Expression → RAS Generation → MAREA → Enriched Pathway Maps
44 3. **RAS/RPS Enrichment Analysis**: RAS + RPS computation → MAREA → Enriched Maps 44
45 2. **Flux Sampling Analysis**:
46 Gene Expression → RAS Generation → RAS to Bounds → Flux Simulation → Flux to Map → Flux-enriched Maps
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48 3. **RAS+RPS Combined Enrichment**:
49 Gene Expression + Metabolite Data → RAS + RPS Generation → MAREA → Multi-omics Enriched Maps
45 50
46 ## Community & Support 51 ## Community & Support
47 52
48 - **Documentation**: Complete guides and API reference 53 - **Documentation**: Complete guides and references
49 - **Discussions**: Ask questions and share experiences 54 - **Issues**: Report bugs and request features on [GitHub](https://github.com/CompBtBs/COBRAxy/issues)
50 - **Issues**: Report bugs and request features
51 - **Contributing**: Help improve COBRAxy 55 - **Contributing**: Help improve COBRAxy
52 56
53 ## Quick Links
54
55 | Resource | Description |
56 |----------|-------------|
57 | [Installation Guide](installation.md) | Get COBRAxy running on your system |
58 | [Galaxy Tutorial](tutorials/galaxy-setup.md) | Web-based analysis setup |
59 | [Python Tutorial](tutorials/python-api.md) | Use COBRAxy programmatically |
60 | [Tools Documentation](tools/) | Complete tool reference |
61
62 ---
63
64 **Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running! 57 **Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running!