Mercurial > repos > bimib > cobraxy
comparison COBRAxy/docs/quickstart.md @ 492:4ed95023af20 draft
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author | francesco_lapi |
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date | Tue, 30 Sep 2025 14:02:17 +0000 |
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1 # Quick Start Guide | |
2 | |
3 Get started with COBRAxy! This guide walks you through your first metabolic analysis. | |
4 | |
5 ## Step 1: Verify Installation | |
6 | |
7 Test that COBRAxy is working: | |
8 | |
9 ```bash | |
10 # Check if tools are available | |
11 ras_generator --help | |
12 | |
13 # Should display help text without errors | |
14 ``` | |
15 | |
16 ## Step 2: Download Sample Data | |
17 | |
18 Create a sample gene expression file: | |
19 | |
20 ```bash | |
21 # Create sample data | |
22 cat > sample_expression.tsv << 'EOF' | |
23 Gene_ID Control_1 Control_2 Treatment_1 Treatment_2 | |
24 HGNC:5 8.5 9.2 15.7 14.3 | |
25 HGNC:10 3.2 4.1 8.8 7.9 | |
26 HGNC:15 7.9 8.2 4.4 5.1 | |
27 HGNC:25 12.1 13.5 18.2 17.8 | |
28 HGNC:30 6.3 7.1 11.5 10.8 | |
29 HGNC:55 14.2 15.8 22.1 21.3 | |
30 HGNC:80 5.7 6.4 2.8 3.2 | |
31 HGNC:100 9.8 10.5 16.7 15.9 | |
32 EOF | |
33 ``` | |
34 | |
35 ## Step 3: Generate Activity Scores | |
36 | |
37 Compute Reaction Activity Scores (RAS) from your gene expression: | |
38 | |
39 ```bash | |
40 # Generate RAS scores using built-in ENGRO2 model | |
41 ras_generator -td $(pwd) \ | |
42 -in sample_expression.tsv \ | |
43 -ra ras_scores.tsv \ | |
44 -rs ENGRO2 | |
45 | |
46 # Check output | |
47 head ras_scores.tsv | |
48 ``` | |
49 | |
50 **Expected output**: | |
51 ```tsv | |
52 Reactions Control_1 Control_2 Treatment_1 Treatment_2 | |
53 R_HEX1 8.5 9.2 15.7 14.3 | |
54 R_PGI 7.9 8.2 4.4 5.1 | |
55 ... | |
56 ``` | |
57 | |
58 ## Step 4: Create Pathway Visualizations | |
59 | |
60 Generate enriched pathway maps with statistical analysis: | |
61 | |
62 ```bash | |
63 # Create pathway maps with statistical analysis | |
64 marea -td $(pwd) \ | |
65 -using_RAS true \ | |
66 -input_data ras_scores.tsv \ | |
67 -choice_map ENGRO2 \ | |
68 -gs true \ | |
69 -idop pathway_maps | |
70 | |
71 # Check results | |
72 ls pathway_maps/ | |
73 ``` | |
74 | |
75 **Expected output**: SVG files with colored pathway maps showing metabolic changes. | |
76 | |
77 ## Step 5: View Results | |
78 | |
79 Open the generated pathway maps: | |
80 | |
81 ```bash | |
82 # Open SVG files in your browser or image viewer | |
83 # Files will be in pathway_maps/ directory | |
84 firefox pathway_maps/*.svg # Linux | |
85 open pathway_maps/*.svg # macOS | |
86 ``` | |
87 | |
88 ## What Just Happened? | |
89 | |
90 1. **RAS Generation**: Mapped gene expression to metabolic reactions using GPR rules | |
91 2. **Statistical Analysis**: Identified significantly altered pathways between conditions | |
92 3. **Visualization**: Created colored pathway maps highlighting metabolic changes | |
93 | |
94 ## Next Steps | |
95 | |
96 ### Learn More About the Analysis | |
97 | |
98 - **[Understanding RAS](tools/ras-generator.md)** - How activity scores are computed | |
99 - **[MAREA Analysis](tools/marea.md)** - Statistical enrichment methods | |
100 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview | |
101 | |
102 ### Try Advanced Features | |
103 | |
104 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions | |
105 - **[Python API](tutorials/python-api.md)** - Integrate into scripts and pipelines | |
106 - **[Galaxy Interface](tutorials/galaxy-setup.md)** - Web-based analysis | |
107 | |
108 ### Use Your Own Data | |
109 | |
110 - **[Data Formats](tutorials/data-formats.md)** - Prepare your expression data | |
111 - **[Troubleshooting](troubleshooting.md)** - Common issues and solutions | |
112 | |
113 ## Complete Example Pipeline | |
114 | |
115 Here's the full command sequence for reference: | |
116 | |
117 ```bash | |
118 # Set up | |
119 cd /path/to/analysis/ | |
120 | |
121 # Generate sample data (or use your own) | |
122 cat > expression.tsv << 'EOF' | |
123 [your gene expression data] | |
124 EOF | |
125 | |
126 # Run analysis pipeline | |
127 ras_generator -td /path/to/COBRAxy -in expression.tsv -ra ras.tsv -rs ENGRO2 | |
128 marea -td /path/to/COBRAxy -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps | |
129 | |
130 # View results | |
131 ls maps/*.svg | |
132 ``` | |
133 | |
134 ## Getting Help | |
135 | |
136 If something doesn't work: | |
137 | |
138 1. **Check Prerequisites**: Ensure COBRAxy is properly installed | |
139 2. **Verify File Format**: Make sure your data is tab-separated TSV | |
140 3. **Review Logs**: Look for error messages in the terminal output | |
141 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! |