Mercurial > repos > bimib > cobraxy

comparison COBRAxy/docs/quickstart.md @ 542:fcdbc81feb45 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
parents 4ed95023af20
children
comparison
equal deleted inserted replaced
541:fa93040a75af 542:fcdbc81feb45
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 ras_generator -td $(pwd) \ 41 # Note: -td is optional and auto-detected after pip install
42 ras_generator \
42 -in sample_expression.tsv \ 43 -in sample_expression.tsv \
43 -ra ras_scores.tsv \ 44 -ra ras_scores.tsv \
44 -rs ENGRO2 45 -rs ENGRO2
45 46
46 # Check output 47 # Check output
59 60
60 Generate enriched pathway maps with statistical analysis: 61 Generate enriched pathway maps with statistical analysis:
61 62
62 ```bash 63 ```bash
63 # Create pathway maps with statistical analysis 64 # Create pathway maps with statistical analysis
64 marea -td $(pwd) \ 65 # Note: -td is optional and auto-detected after pip install
66 marea \
65 -using_RAS true \ 67 -using_RAS true \
66 -input_data ras_scores.tsv \ 68 -input_data ras_scores.tsv \
67 -choice_map ENGRO2 \ 69 -choice_map ENGRO2 \
68 -gs true \ 70 -gs true \
69 -idop pathway_maps 71 -idop pathway_maps
93 95
94 ## Next Steps 96 ## Next Steps
95 97
96 ### Learn More About the Analysis 98 ### Learn More About the Analysis
97 99
98 - **[Understanding RAS](tools/ras-generator.md)** - How activity scores are computed 100 - **[Understanding RAS](/tools/ras-generator.md)** - How activity scores are computed
99 - **[MAREA Analysis](tools/marea.md)** - Statistical enrichment methods 101 - **[MAREA Analysis](/tools/marea.md)** - Statistical enrichment methods
100 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview 102 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview
101 103
102 ### Try Advanced Features 104 ### Try Advanced Features
103 105
104 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions 106 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions
105 - **[Python API](tutorials/python-api.md)** - Integrate into scripts and pipelines 107 - **[Galaxy Interface](/tutorials/galaxy-setup.md)** - Web-based analysis
106 - **[Galaxy Interface](tutorials/galaxy-setup.md)** - Web-based analysis
107 108
108 ### Use Your Own Data 109 ### Use Your Own Data
109 110
110 - **[Data Formats](tutorials/data-formats.md)** - Prepare your expression data 111 - **[Data Formats](/tutorials/data-formats.md)** - Prepare your expression data
111 - **[Troubleshooting](troubleshooting.md)** - Common issues and solutions 112 - **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
112 113
113 ## Complete Example Pipeline 114 ## Complete Example Pipeline
114 115
115 Here's the full command sequence for reference: 116 Here's the full command sequence for reference:
116 117
122 cat > expression.tsv << 'EOF' 123 cat > expression.tsv << 'EOF'
123 [your gene expression data] 124 [your gene expression data]
124 EOF 125 EOF
125 126
126 # Run analysis pipeline 127 # Run analysis pipeline
127 ras_generator -td /path/to/COBRAxy -in expression.tsv -ra ras.tsv -rs ENGRO2 128 # Note: -td is optional and auto-detected after pip install
128 marea -td /path/to/COBRAxy -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps 129 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
129 131
130 # View results 132 # View results
131 ls maps/*.svg 133 ls maps/*.svg
132 ``` 134 ```
133 135
136 If something doesn't work: 138 If something doesn't work:
137 139
138 1. **Check Prerequisites**: Ensure COBRAxy is properly installed 140 1. **Check Prerequisites**: Ensure COBRAxy is properly installed
139 2. **Verify File Format**: Make sure your data is tab-separated TSV 141 2. **Verify File Format**: Make sure your data is tab-separated TSV
140 3. **Review Logs**: Look for error messages in the terminal output 142 3. **Review Logs**: Look for error messages in the terminal output
141 4. **Consult Guides**: [Troubleshooting](troubleshooting.md) and [Installation](installation.md) 143 4. **Consult Guides**: [Troubleshooting](/troubleshooting.md) and [Installation](/installation.md)
142
143 **Still stuck?** Ask for help in [GitHub Discussions](https://github.com/CompBtBs/COBRAxy/discussions).
144
145 ## Summary
146
147 🎉 **Congratulations!** You've completed your first COBRAxy analysis. You now know how to:
148
149 - ✅ Generate metabolic activity scores from gene expression
150 - ✅ Create statistical pathway visualizations
151 - ✅ Interpret basic COBRAxy outputs
152
153 Ready for more? Explore the [full documentation](/) to unlock COBRAxy's complete potential!