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comparison COBRAxy/docs/getting-started.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
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 # Note: -td is optional and auto-detected after pip install
78 ras_generator \ 77 ras_generator \
79 -in expression_data.tsv \ 78 -in expression_data.tsv \
80 -ra ras_output.tsv \ 79 -ra ras_output.tsv \
81 -rs ENGRO2 80 -rs ENGRO2
82 ``` 81 ```
83 82
84 ### Step 3: Create Pathway Maps 83 ### Step 3: Create Pathway Maps
85 84
86 ```bash 85 ```bash
87 # Generate enriched pathway maps 86 # Generate enriched pathway maps
88 # Note: -td is optional and auto-detected after pip install
89 marea \ 87 marea \
90 -using_RAS true \ 88 -using_RAS true \
91 -input_data ras_output.tsv \ 89 -input_data ras_output.tsv \
92 -choice_map ENGRO2 \ 90 -choice_map ENGRO2 \
93 -gs true \ 91 -gs true \
136 134
137 ## Next Steps 135 ## Next Steps
138 136
139 Now that you understand the basics: 137 Now that you understand the basics:
140 138
141 1. **[Quick Start Guide](/quickstart.md)** - Complete walkthrough with example data 139 1. **[Quick Start Guide](quickstart)** - Complete walkthrough with example data
142 2. **[Galaxy Tutorial](/tutorials/galaxy-setup.md)** - Web-based analysis setup 140 2. **[Galaxy Tutorial](tutorials/galaxy-setup)** - Web-based analysis setup
143 3. **[Tools Reference](/tools/)** - Detailed documentation for each tool 141 3. **[Tools Reference](/tools/)** - Detailed documentation for each tool
144 4. **[Examples](/examples/)** - Real-world analysis examples
145 142
146 ## Need Help? 143 ## Need Help?
147 144
148 - **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions 145 - **[Troubleshooting](troubleshooting)** - Common issues and solutions
149 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions 146 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
150 - **[Contributing](/contributing.md)** - Help improve COBRAxy 147 - **[Contributing](contributing)** - Help improve COBRAxy