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1 # COBRAxy Documentation 1 # COBRAxy Documentation
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3 > A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration. 3 > A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration.
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5 COBRAxy transforms gene expression and metabolite data into meaningful metabolic insights through flux sampling and interactive pathway maps. 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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7 ## Overview 7 ## Overview
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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. 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
11 composition information to refine flux predictions. Additionally, COBRAxy provides a user-friendly interface
12 for visualizing significant flux differences between populations on an enriched metabolic map. This
13 extension provides a comprehensive and accessible framework for advanced metabolic analysis, enabling
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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11 ## Key Features 18 ## Key Features
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20 - **Galaxy Tools** - Web-based analysis with intuitive interface
13 - **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data 21 - **Reaction Activity Scores (RAS)** - Compute metabolic activity from gene expression data
14 - **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance 22 - **Reaction Propensity Scores (RPS)** - Infer metabolic preferences from metabolite abundance
15 - **Flux Sampling** - Sample metabolic flux distributions with CBS or OptGP algorithms 23 - **Flux computation** - Compute metabolic flux distributions using different optimization or sampling algorithms
16 - **Statistical Analysis** - Perform pFBA, FVA, and sensitivity analysis 24 - **Statistical Analysis** - Perform statistically significant flux differences between groups of samples and report on an enriched metabolic map
17 - **Interactive Maps** - Generate publication-ready pathway visualizations with SVG/PDF export 25 - **Built-in Models** - Ready-to-use models including ENGRO2 and Recon3D
18 - **Galaxy Tools** - Web-based analysis with intuitive interface
19 - **Built-in Models** - Ready-to-use models including ENGRO2 and Recon
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21 ## Quick Navigation 27 ## Quick Navigation
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23 ### [Installation](installation.md) 29 ### [Installation](installation.md)
24 Install COBRAxy and get it running on your system 30 Install COBRAxy and get it running on your system
29 ### [Tools Documentation](tools/) 35 ### [Tools Documentation](tools/)
30 Complete reference for all COBRAxy tools 36 Complete reference for all COBRAxy tools
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32 ## Data Flow 38 ## Data Flow
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34 COBRAxy follows two parallel analysis paths: 40 COBRAxy follows several analysis paths:
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36 1. **Enrichment Analysis**: RAS + RPS → MAREA → Enriched Maps 42 1. **RAS Enrichment Analysis**: RAS computation → MAREA → Enriched Maps
37 2. **Flux Simulation**: RAS → Model Constraints → Flux Sampling → Flux Maps 43 2. **Flux Enrichment Analysis Simulation**: RAS computation → Model Constraints → Flux Sampling → Flux Maps
44 3. **RAS/RPS Enrichment Analysis**: RAS + RPS computation → MAREA → Enriched Maps
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39 ## Community & Support 46 ## Community & Support
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41 - **Documentation**: Complete guides and API reference 48 - **Documentation**: Complete guides and API reference
42 - **Discussions**: Ask questions and share experiences 49 - **Discussions**: Ask questions and share experiences