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comparison COBRAxy/docs/getting-started.md @ 542:fcdbc81feb45 draft

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
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72 72
73 ### Step 2: Generate Activity Scores 73 ### Step 2: Generate Activity Scores
74 74
75 ```bash 75 ```bash
76 # Generate RAS from expression data 76 # Generate RAS from expression data
77 ras_generator -td $(pwd) \ 77 # Note: -td is optional and auto-detected after pip install
78 ras_generator \
78 -in expression_data.tsv \ 79 -in expression_data.tsv \
79 -ra ras_output.tsv \ 80 -ra ras_output.tsv \
80 -rs ENGRO2 81 -rs ENGRO2
81 ``` 82 ```
82 83
83 ### Step 3: Create Pathway Maps 84 ### Step 3: Create Pathway Maps
84 85
85 ```bash 86 ```bash
86 # Generate enriched pathway maps 87 # Generate enriched pathway maps
87 marea -td $(pwd) \ 88 # Note: -td is optional and auto-detected after pip install
89 marea \
88 -using_RAS true \ 90 -using_RAS true \
89 -input_data ras_output.tsv \ 91 -input_data ras_output.tsv \
90 -choice_map ENGRO2 \ 92 -choice_map ENGRO2 \
91 -gs true \ 93 -gs true \
92 -idop pathway_maps 94 -idop pathway_maps
106 | Model | Organism | Reactions | Genes | Description | 108 | Model | Organism | Reactions | Genes | Description |
107 |-------|----------|-----------|-------|-------------| 109 |-------|----------|-----------|-------|-------------|
108 | **ENGRO2** | Human | ~2,000 | ~500 | Focused human metabolism model | 110 | **ENGRO2** | Human | ~2,000 | ~500 | Focused human metabolism model |
109 | **Recon** | Human | ~10,000 | ~2,000 | Comprehensive human metabolism | 111 | **Recon** | Human | ~10,000 | ~2,000 | Comprehensive human metabolism |
110 112
111 Models are stored in the `local/` directory and include: 113 Models are stored in the `src/local/` directory and include:
112 - SBML files 114 - SBML files
113 - GPR rules 115 - GPR rules
114 - Gene mapping tables 116 - Gene mapping tables
115 - Pathway templates 117 - Pathway templates
116 118
130 glucose 100.5 85.3 120.7 132 glucose 100.5 85.3 120.7
131 pyruvate 45.2 38.1 52.8 133 pyruvate 45.2 38.1 52.8
132 lactate 23.9 41.2 19.4 134 lactate 23.9 41.2 19.4
133 ``` 135 ```
134 136
135 ## Command Line vs Python API
136
137 COBRAxy offers two usage modes:
138
139 ### Command Line (Quick Analysis)
140 ```bash
141 # Simple command-line execution
142 ras_generator -td $(pwd) -in data.tsv -ra output.tsv -rs ENGRO2
143 ```
144
145 ### Python API (Programming)
146 ```python
147 import ras_generator
148 # Call main function with arguments
149 ras_generator.main(['-td', '/path', '-in', 'data.tsv', '-ra', 'output.tsv', '-rs', 'ENGRO2'])
150 ```
151
152 ## Next Steps 137 ## Next Steps
153 138
154 Now that you understand the basics: 139 Now that you understand the basics:
155 140
156 1. **[Quick Start Guide](quickstart.md)** - Complete walkthrough with example data 141 1. **[Quick Start Guide](/quickstart.md)** - Complete walkthrough with example data
157 2. **[Python API Tutorial](tutorials/python-api.md)** - Learn programmatic usage 142 2. **[Galaxy Tutorial](/tutorials/galaxy-setup.md)** - Web-based analysis setup
158 3. **[Tools Reference](tools/)** - Detailed documentation for each tool 143 3. **[Tools Reference](/tools/)** - Detailed documentation for each tool
159 4. **[Examples](examples/)** - Real-world analysis examples 144 4. **[Examples](/examples/)** - Real-world analysis examples
160 145
161 ## Need Help? 146 ## Need Help?
162 147
163 - **[Troubleshooting](troubleshooting.md)** - Common issues and solutions 148 - **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
164 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions 149 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
165 - **[Contributing](contributing.md)** - Help improve COBRAxy 150 - **[Contributing](/contributing.md)** - Help improve COBRAxy