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comparison COBRAxy/docs/quickstart.md @ 547:73f2f7e2be17 draft

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author francesco_lapi
date Tue, 28 Oct 2025 10:44:07 +0000
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546:01147e83f43c 547:73f2f7e2be17
36 36
37 Compute Reaction Activity Scores (RAS) from your gene expression: 37 Compute Reaction Activity Scores (RAS) from your gene expression:
38 38
39 ```bash 39 ```bash
40 # Generate RAS scores using built-in ENGRO2 model 40 # Generate RAS scores using built-in ENGRO2 model
41 # Note: -td is optional and auto-detected after pip install
42 ras_generator \ 41 ras_generator \
43 -in sample_expression.tsv \ 42 -in sample_expression.tsv \
44 -ra ras_scores.tsv \ 43 -ra ras_scores.tsv \
45 -rs ENGRO2 44 -rs ENGRO2
46 45
60 59
61 Generate enriched pathway maps with statistical analysis: 60 Generate enriched pathway maps with statistical analysis:
62 61
63 ```bash 62 ```bash
64 # Create pathway maps with statistical analysis 63 # Create pathway maps with statistical analysis
65 # Note: -td is optional and auto-detected after pip install
66 marea \ 64 marea \
67 -using_RAS true \ 65 -using_RAS true \
68 -input_data ras_scores.tsv \ 66 -input_data ras_scores.tsv \
69 -choice_map ENGRO2 \ 67 -choice_map ENGRO2 \
70 -gs true \ 68 -gs true \
95 93
96 ## Next Steps 94 ## Next Steps
97 95
98 ### Learn More About the Analysis 96 ### Learn More About the Analysis
99 97
100 - **[Understanding RAS](/tools/ras-generator.md)** - How activity scores are computed 98 - **[Understanding RAS](tools/ras-generator)** - How activity scores are computed
101 - **[MAREA Analysis](/tools/marea.md)** - Statistical enrichment methods 99 - **[MAREA Analysis](tools/marea)** - Statistical enrichment methods
102 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview 100 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview
103 101
104 ### Try Advanced Features 102 ### Try Advanced Features
105 103
106 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions 104 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions
107 - **[Galaxy Interface](/tutorials/galaxy-setup.md)** - Web-based analysis 105 - **[Galaxy Interface](tutorials/galaxy-setup)** - Web-based analysis
108 106
109 ### Use Your Own Data 107 ### Use Your Own Data
110 108
111 - **[Data Formats](/tutorials/data-formats.md)** - Prepare your expression data 109 - **[Data Formats](tutorials/data-formats)** - Prepare your expression data
112 - **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions 110 - **[Troubleshooting](troubleshooting)** - Common issues and solutions
113 111
114 ## Complete Example Pipeline 112 ## Complete Example Pipeline
115 113
116 Here's the full command sequence for reference: 114 Here's the full command sequence for reference:
117 115
123 cat > expression.tsv << 'EOF' 121 cat > expression.tsv << 'EOF'
124 [your gene expression data] 122 [your gene expression data]
125 EOF 123 EOF
126 124
127 # Run analysis pipeline 125 # Run analysis pipeline
128 # Note: -td is optional and auto-detected after pip install
129 ras_generator -in expression.tsv -ra ras.tsv -rs ENGRO2 126 ras_generator -in expression.tsv -ra ras.tsv -rs ENGRO2
130 marea -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps 127 marea -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps
131 128
132 # View results 129 # View results
133 ls maps/*.svg 130 ls maps/*.svg
138 If something doesn't work: 135 If something doesn't work:
139 136
140 1. **Check Prerequisites**: Ensure COBRAxy is properly installed 137 1. **Check Prerequisites**: Ensure COBRAxy is properly installed
141 2. **Verify File Format**: Make sure your data is tab-separated TSV 138 2. **Verify File Format**: Make sure your data is tab-separated TSV
142 3. **Review Logs**: Look for error messages in the terminal output 139 3. **Review Logs**: Look for error messages in the terminal output
143 4. **Consult Guides**: [Troubleshooting](/troubleshooting.md) and [Installation](/installation.md) 140 4. **Consult Guides**: [Troubleshooting](troubleshooting) and [Installation](installation)