comparison COBRAxy/docs/tools/README.md @ 542:fcdbc81feb45 draft

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## Available Tools

| Tool | Purpose | Input | Output |
|------|---------|--------|--------|
| [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
| [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values |
| [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
| [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
| [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions |
| [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
| [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data |
| [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |

## Common Parameters

All tools share these basic parameters:

- **`-td, --tool_dir`**: COBRAxy installation directory (required)
- **`-in, --input`**: Input dataset file
- **`-idop, --output_dir`**: Output directory for results
- **`-rs, --rules_selector`**: Built-in model (ENGRO2, Recon, HMRcore)

## Analysis Workflows

**Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps

## Tool Selection Guide

### Choose Your Analysis Path

**For Pathway Enrichment**
1. [RAS Generator](ras-generator.md) → Generate activity scores
2. [RPS Generator](rps-generator.md) → Generate propensity scores (optional)
3. [MAREA](marea.md) → Statistical analysis and visualization

**For Flux Analysis**  
1. [RAS Generator](ras-generator.md) → Generate activity scores
2. [RAS to Bounds](ras-to-bounds.md) → Apply constraints
3. [Flux Simulation](flux-simulation.md) → Sample fluxes
4. [Flux to Map](flux-to-map.md) → Create visualizations

**For Model Exploration**
1. [Model Setting](metabolic-model-setting.md) → Extract model info
2. Analyze model structure and gene coverage

**For Sample Classification**
1. Generate RAS/RPS scores
2. [MAREA Cluster](marea-cluster.md) → Cluster samples



## Troubleshooting

### Common Issues Across Tools

**File Path Problems**
- Use absolute paths when possible
- Ensure all input files exist before starting
- Check write permissions for output directories

**File Issues**
- Check file paths and permissions
- Verify input file formats
- Ensure sufficient disk space

**Model Issues**
- Verify model file format and gene ID consistency
- Check gene ID mapping between data and model
- Use built-in models to avoid compatibility issues

For tool-specific issues:
1. Check individual tool documentation
2. Review parameter requirements and formats
3. Test with smaller datasets first
4. Consult [troubleshooting guide](../troubleshooting.md)

## Contributing

Help improve tool documentation:
- Report unclear instructions

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## Available Tools

| Tool | Purpose | Input | Output |
|------|---------|--------|--------|
| [Import Metabolic Model](tools/import-metabolic-model) | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
| [Export Metabolic Model](tools/export-metabolic-model) | Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
| [RAS Generator](tools/ras-generator) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
| [RPS Generator](tools/rps-generator) | Compute reaction propensity scores | Metabolite abundance | RPS values |
| [MAREA](tools/marea) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
| [RAS to Bounds](tools/ras-to-bounds) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
| [Flux Simulation](tools/flux-simulation) | Sample metabolic fluxes | Constrained model | Flux distributions |
| [Flux to Map](tools/flux-to-map) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
| [MAREA Cluster](tools/marea-cluster) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |


## Analysis Workflows

**Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps

## Tool Selection Guide

### Choose Your Analysis Path

**For Pathway Enrichment**
1. [RAS Generator](tools/ras-generator) → Generate activity scores
2. [RPS Generator](tools/rps-generator) → Generate propensity scores (optional)
3. [MAREA](tools/marea) → Statistical analysis and visualization

**For Flux Analysis**  
1. [RAS Generator](tools/ras-generator) → Generate activity scores
2. [RAS to Bounds](tools/ras-to-bounds) → Apply constraints
3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
4. [Flux to Map](tools/flux-to-map) → Create visualizations

**For Model Exploration**
1. [Import Metabolic Model](tools/import-metabolic-model) → Extract model info
2. Analyze model structure and gene coverage

**For Model Creation**
1. Create/edit tabular model data
2. [Export Metabolic Model](tools/export-metabolic-model) → Create SBML/JSON/MAT/YAML model

**For Sample Classification**
1. Generate RAS/RPS scores
2. [MAREA Cluster](tools/marea-cluster) → Cluster samples



## Troubleshooting

### Common Issues Across Tools

**Model Issues**
- Verify model file format and gene ID consistency
- Check gene ID mapping between data and model
- Use built-in models to avoid compatibility issues

For tool-specific issues:
1. Check individual tool documentation
2. Review parameter requirements and formats
3. Test with smaller datasets first
4. Consult [troubleshooting guide](/troubleshooting.md)

## Contributing

Help improve tool documentation:
- Report unclear instructions