--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/docs/tools/marea.md	Tue Sep 30 14:02:17 2025 +0000
@@ -0,0 +1,279 @@
+# MAREA
+
+Metabolic Reaction Enrichment Analysis for statistical comparison and map visualization.
+
+## Overview
+
+MAREA performs statistical enrichment analysis on RAS/RPS data to identify significantly different metabolic reactions between sample groups. It generates enriched pathway maps with color-coded reactions showing statistical significance and fold changes.
+
+## Usage
+
+### Command Line
+
+```bash
+marea -td /path/to/COBRAxy \
+      -using_RAS true \
+      -input_data ras_data.tsv \
+      -input_class class_labels.tsv \
+      -comparison manyvsmany \
+      -test ks \
+      -pv 0.05 \
+      -fc 1.5 \
+      -choice_map ENGRO2 \
+      -generate_svg true \
+      -idop results/
+```
+
+### Galaxy Interface
+
+Select "MAREA" from the COBRAxy tool suite and configure analysis parameters through the web interface.
+
+## Parameters
+
+### Required Parameters
+
+| Parameter | Flag | Description |
+|-----------|------|-------------|
+| Tool Directory | `-td, --tool_dir` | Path to COBRAxy installation directory |
+
+### Data Input Parameters
+
+| Parameter | Flag | Description | Default |
+|-----------|------|-------------|---------|
+| Use RAS | `-using_RAS, --using_RAS` | Include RAS analysis | true |
+| RAS Data | `-input_data, --input_data` | RAS scores TSV file | - |
+| RAS Classes | `-input_class, --input_class` | Sample group labels | - |
+| Multiple RAS | `-input_datas, --input_datas` | Multiple RAS files (space-separated) | - |
+| RAS Names | `-names, --names` | Names for multiple datasets | - |
+| Use RPS | `-using_RPS, --using_RPS` | Include RPS analysis | false |
+| RPS Data | `-input_data_rps, --input_data_rps` | RPS scores TSV file | - |
+| RPS Classes | `-input_class_rps, --input_class_rps` | RPS sample groups | - |
+
+### Statistical Parameters
+
+| Parameter | Flag | Description | Default |
+|-----------|------|-------------|---------|
+| Comparison Type | `-co, --comparison` | Statistical comparison mode | manyvsmany |
+| Statistical Test | `-te, --test` | Statistical test method | ks |
+| P-Value Threshold | `-pv, --pValue` | Significance threshold | 0.1 |
+| Adjusted P-values | `-adj, --adjusted` | Apply FDR correction | false |
+| Fold Change | `-fc, --fChange` | Minimum fold change | 1.5 |
+| Net Enrichment | `-ne, --net` | Use net enrichment for RPS | false |
+| Analysis Option | `-op, --option` | Analysis mode | datasets |
+
+### Visualization Parameters
+
+| Parameter | Flag | Description | Default |
+|-----------|------|-------------|---------|
+| Map Choice | `-choice_map, --choice_map` | Built-in metabolic map | - |
+| Custom Map | `-custom_map, --custom_map` | Path to custom SVG map | - |
+| Generate SVG | `-gs, --generate_svg` | Create SVG output | true |
+| Generate PDF | `-gp, --generate_pdf` | Create PDF output | false |
+| Generate PNG | `-gpng, --generate_png` | Create PNG output | false |
+| Color Map | `-colorm, --color_map` | Color scheme (jet/viridis) | jet |
+| Output Directory | `-idop, --output_path` | Results directory | result/ |
+
+### Advanced Parameters
+
+| Parameter | Flag | Description | Default |
+|-----------|------|-------------|---------|
+| Output Log | `-ol, --out_log` | Log file path | - |
+| Control Sample | `-on, --control` | Control group identifier | - |
+
+## Input Formats
+
+### RAS/RPS Data File
+
+Tab-separated format with reactions as rows and samples as columns:
+
+```
+Reaction	Sample1	Sample2	Sample3	Sample4
+R00001	1.25	0.85	1.42	0.78
+R00002	0.65	1.35	0.72	1.28
+R00003	2.15	2.05	0.45	0.52
+```
+
+### Class Labels File
+
+Sample grouping information:
+
+```
+Sample	Class
+Sample1	Control
+Sample2	Treatment
+Sample3	Control
+Sample4	Treatment
+```
+
+## Comparison Types
+
+### manyvsmany
+Compare all possible pairs of groups:
+- Group A vs Group B
+- Group A vs Group C  
+- Group B vs Group C
+
+### onevsrest
+Compare each group against all others combined:
+- Group A vs (Group B + Group C)
+- Group B vs (Group A + Group C)
+
+### onevsmany
+Compare one specific group against each other group separately:
+- Control vs Treatment1
+- Control vs Treatment2
+
+## Statistical Tests
+
+| Test | Description | Use Case |
+|------|-------------|----------|
+| `ks` | Kolmogorov-Smirnov | Non-parametric, distribution-free |
+| `ttest_p` | Paired t-test | Related samples |
+| `ttest_ind` | Independent t-test | Unrelated samples |
+| `wilcoxon` | Wilcoxon signed-rank | Non-parametric paired |
+| `mw` | Mann-Whitney U | Non-parametric independent |
+| `DESeq` | DESeq2-style analysis | Count-like data with dispersion |
+
+## Output Files
+
+### Statistical Results
+- `comparison_stats.tsv`: P-values, fold changes, and test statistics
+- `enriched_reactions.tsv`: Significantly enriched reactions only
+- `comparison_summary.txt`: Analysis summary and parameters
+
+### Visualization
+- `pathway_map.svg`: Color-coded metabolic map
+- `pathway_map.pdf`: PDF version (if requested)
+- `pathway_map.png`: PNG version (if requested)
+- `legend.svg`: Color scale and significance indicators
+
+## Examples
+
+### Basic RAS Analysis
+
+```bash
+# Simple two-group comparison
+marea -td /opt/COBRAxy \
+      -using_RAS true \
+      -input_data ras_scores.tsv \
+      -input_class sample_groups.tsv \
+      -comparison manyvsmany \
+      -test ks \
+      -pv 0.05 \
+      -choice_map ENGRO2 \
+      -idop results/
+```
+
+### Combined RAS + RPS Analysis
+
+```bash
+# Multi-modal analysis
+marea -td /opt/COBRAxy \
+      -using_RAS true \
+      -input_data ras_scores.tsv \
+      -input_class ras_groups.tsv \
+      -using_RPS true \
+      -input_data_rps rps_scores.tsv \
+      -input_class_rps rps_groups.tsv \
+      -comparison onevsrest \
+      -test DESeq \
+      -adj true \
+      -fc 2.0 \
+      -choice_map HMRcore \
+      -generate_pdf true \
+      -idop multimodal_results/
+```
+
+### Multiple Dataset Analysis
+
+```bash
+# Compare multiple experiments
+marea -td /opt/COBRAxy \
+      -using_RAS true \
+      -input_datas exp1_ras.tsv exp2_ras.tsv exp3_ras.tsv \
+      -names "Experiment1" "Experiment2" "Experiment3" \
+      -comparison onevsmany \
+      -test wilcoxon \
+      -pv 0.01 \
+      -custom_map custom_pathway.svg \
+      -idop multi_experiment/
+```
+
+## Map Visualization
+
+### Built-in Maps
+- **ENGRO2**: Human genome-scale reconstruction
+- **HMRcore**: Core human metabolic network  
+- **Recon**: Recon3D human model
+
+### Color Coding
+- **Red**: Significantly upregulated (high activity)
+- **Blue**: Significantly downregulated (low activity)
+- **Gray**: Not significant
+- **Line Width**: Proportional to fold change magnitude
+
+### Custom Maps
+SVG files with reaction elements having IDs matching your data:
+```xml
+<rect id="R00001" class="reaction" .../>
+<path id="R00002" class="reaction" .../>
+```
+
+## Quality Control
+
+### Pre-analysis Checks
+- Verify sample names match between data and class files
+- Check for missing values and outliers
+- Ensure adequate sample sizes per group (n ≥ 3 recommended)
+
+### Post-analysis Validation
+- Review statistical distribution assumptions
+- Check multiple testing correction effects
+- Validate biological relevance of enriched pathways
+
+## Tips and Best Practices
+
+### Statistical Considerations
+- Use FDR correction (`-adj true`) for multiple comparisons
+- Choose appropriate tests based on data distribution
+- Consider effect size alongside significance
+
+### Visualization Optimization
+- Use high fold change thresholds (>2.0) for cleaner maps
+- Export both SVG (editable) and PDF (publication-ready) formats
+- Adjust color schemes for colorblind accessibility
+
+## Troubleshooting
+
+### Common Issues
+
+**No significant reactions found**
+- Lower p-value threshold (`-pv 0.1`)
+- Reduce fold change requirement (`-fc 1.2`)
+- Check sample group definitions
+
+**Map rendering errors**
+- Verify SVG map file integrity
+- Check reaction ID matching between data and map
+- Ensure sufficient system memory for large maps
+
+**Statistical test failures**
+- Verify data normality for parametric tests
+- Check for sufficient sample sizes
+- Consider alternative test methods
+
+## Integration
+
+### Upstream Tools
+- [RAS Generator](ras-generator.md) - Generate RAS scores
+- [RPS Generator](rps-generator.md) - Generate RPS scores
+
+### Downstream Analysis
+- [Flux to Map](flux-to-map.md) - Additional visualization options
+- [MAREA Cluster](marea-cluster.md) - Sample clustering analysis
+
+## See Also
+
+- [Statistical Tests Documentation](../tutorials/statistical-tests.md)
+- [Map Customization Guide](../tutorials/custom-maps.md)
+- [Multi-modal Analysis Tutorial](../tutorials/multimodal-analysis.md)
\ No newline at end of file