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

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### Step 2: Generate Activity Scores

```bash
# Generate RAS from expression data
ras_generator -td $(pwd) \
  -in expression_data.tsv \
  -ra ras_output.tsv \
  -rs ENGRO2
```

### Step 3: Create Pathway Maps

```bash
# Generate enriched pathway maps
marea -td $(pwd) \
  -using_RAS true \
  -input_data ras_output.tsv \
  -choice_map ENGRO2 \
  -gs true \
  -idop pathway_maps

| Model | Organism | Reactions | Genes | Description |
|-------|----------|-----------|-------|-------------|
| **ENGRO2** | Human | ~2,000 | ~500 | Focused human metabolism model |
| **Recon** | Human | ~10,000 | ~2,000 | Comprehensive human metabolism |

Models are stored in the `local/` directory and include:
- SBML files
- GPR rules  
- Gene mapping tables
- Pathway templates

glucose	100.5	85.3	120.7
pyruvate	45.2	38.1	52.8
lactate	23.9	41.2	19.4
```

## Command Line vs Python API

COBRAxy offers two usage modes:

### Command Line (Quick Analysis)
```bash
# Simple command-line execution
ras_generator -td $(pwd) -in data.tsv -ra output.tsv -rs ENGRO2
```

### Python API (Programming)
```python
import ras_generator
# Call main function with arguments
ras_generator.main(['-td', '/path', '-in', 'data.tsv', '-ra', 'output.tsv', '-rs', 'ENGRO2'])
```

## Next Steps

Now that you understand the basics:

1. **[Quick Start Guide](quickstart.md)** - Complete walkthrough with example data
2. **[Python API Tutorial](tutorials/python-api.md)** - Learn programmatic usage
3. **[Tools Reference](tools/)** - Detailed documentation for each tool
4. **[Examples](examples/)** - Real-world analysis examples

## Need Help?

- **[Troubleshooting](troubleshooting.md)** - Common issues and solutions
- **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
- **[Contributing](contributing.md)** - Help improve COBRAxy

542:fcdbc81feb45

### Step 2: Generate Activity Scores

```bash
# Generate RAS from expression data
# Note: -td is optional and auto-detected after pip install
ras_generator \
  -in expression_data.tsv \
  -ra ras_output.tsv \
  -rs ENGRO2
```

### Step 3: Create Pathway Maps

```bash
# Generate enriched pathway maps
# Note: -td is optional and auto-detected after pip install
marea \
  -using_RAS true \
  -input_data ras_output.tsv \
  -choice_map ENGRO2 \
  -gs true \
  -idop pathway_maps

| Model | Organism | Reactions | Genes | Description |
|-------|----------|-----------|-------|-------------|
| **ENGRO2** | Human | ~2,000 | ~500 | Focused human metabolism model |
| **Recon** | Human | ~10,000 | ~2,000 | Comprehensive human metabolism |

Models are stored in the `src/local/` directory and include:
- SBML files
- GPR rules  
- Gene mapping tables
- Pathway templates

glucose	100.5	85.3	120.7
pyruvate	45.2	38.1	52.8
lactate	23.9	41.2	19.4
```

## Next Steps

Now that you understand the basics:

1. **[Quick Start Guide](/quickstart.md)** - Complete walkthrough with example data
2. **[Galaxy Tutorial](/tutorials/galaxy-setup.md)** - Web-based analysis setup
3. **[Tools Reference](/tools/)** - Detailed documentation for each tool
4. **[Examples](/examples/)** - Real-world analysis examples

## Need Help?

- **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
- **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
- **[Contributing](/contributing.md)** - Help improve COBRAxy