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

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3 ## Available Tools 3 ## Available Tools
4 4
5 | Tool | Purpose | Input | Output | 5 | Tool | Purpose | Input | Output |
6 |------|---------|--------|--------| 6 |------|---------|--------|--------|
7 | [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values | 7 | [Import Metabolic Model](tools/import-metabolic-model) | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
8 | [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values | 8 | [Export Metabolic Model](tools/export-metabolic-model) | Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
9 | [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics | 9 | [RAS Generator](tools/ras-generator) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
10 | [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds | 10 | [RPS Generator](tools/rps-generator) | Compute reaction propensity scores | Metabolite abundance | RPS values |
11 | [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions | 11 | [MAREA](tools/marea) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
12 | [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps | 12 | [RAS to Bounds](tools/ras-to-bounds) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
13 | [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data | 13 | [Flux Simulation](tools/flux-simulation) | Sample metabolic fluxes | Constrained model | Flux distributions |
14 | [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots | 14 | [Flux to Map](tools/flux-to-map) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
15 | [MAREA Cluster](tools/marea-cluster) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
15 16
16 ## Common Parameters
17
18 All tools share these basic parameters:
19
20 - **`-td, --tool_dir`**: COBRAxy installation directory (required)
21 - **`-in, --input`**: Input dataset file
22 - **`-idop, --output_dir`**: Output directory for results
23 - **`-rs, --rules_selector`**: Built-in model (ENGRO2, Recon, HMRcore)
24 17
25 ## Analysis Workflows 18 ## Analysis Workflows
26 19
27 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps 20 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps
28 21
72 ## Tool Selection Guide 65 ## Tool Selection Guide
73 66
74 ### Choose Your Analysis Path 67 ### Choose Your Analysis Path
75 68
76 **For Pathway Enrichment** 69 **For Pathway Enrichment**
77 1. [RAS Generator](ras-generator.md) → Generate activity scores 70 1. [RAS Generator](tools/ras-generator) → Generate activity scores
78 2. [RPS Generator](rps-generator.md) → Generate propensity scores (optional) 71 2. [RPS Generator](tools/rps-generator) → Generate propensity scores (optional)
79 3. [MAREA](marea.md) → Statistical analysis and visualization 72 3. [MAREA](tools/marea) → Statistical analysis and visualization
80 73
81 **For Flux Analysis** 74 **For Flux Analysis**
82 1. [RAS Generator](ras-generator.md) → Generate activity scores 75 1. [RAS Generator](tools/ras-generator) → Generate activity scores
83 2. [RAS to Bounds](ras-to-bounds.md) → Apply constraints 76 2. [RAS to Bounds](tools/ras-to-bounds) → Apply constraints
84 3. [Flux Simulation](flux-simulation.md) → Sample fluxes 77 3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
85 4. [Flux to Map](flux-to-map.md) → Create visualizations 78 4. [Flux to Map](tools/flux-to-map) → Create visualizations
86 79
87 **For Model Exploration** 80 **For Model Exploration**
88 1. [Model Setting](metabolic-model-setting.md) → Extract model info 81 1. [Import Metabolic Model](tools/import-metabolic-model) → Extract model info
89 2. Analyze model structure and gene coverage 82 2. Analyze model structure and gene coverage
83
84 **For Model Creation**
85 1. Create/edit tabular model data
86 2. [Export Metabolic Model](tools/export-metabolic-model) → Create SBML/JSON/MAT/YAML model
90 87
91 **For Sample Classification** 88 **For Sample Classification**
92 1. Generate RAS/RPS scores 89 1. Generate RAS/RPS scores
93 2. [MAREA Cluster](marea-cluster.md) → Cluster samples 90 2. [MAREA Cluster](tools/marea-cluster) → Cluster samples
94 91
95 92
96 93
97 ## Troubleshooting 94 ## Troubleshooting
98 95
99 ### Common Issues Across Tools 96 ### Common Issues Across Tools
100
101 **File Path Problems**
102 - Use absolute paths when possible
103 - Ensure all input files exist before starting
104 - Check write permissions for output directories
105
106 **File Issues**
107 - Check file paths and permissions
108 - Verify input file formats
109 - Ensure sufficient disk space
110 97
111 **Model Issues** 98 **Model Issues**
112 - Verify model file format and gene ID consistency 99 - Verify model file format and gene ID consistency
113 - Check gene ID mapping between data and model 100 - Check gene ID mapping between data and model
114 - Use built-in models to avoid compatibility issues 101 - Use built-in models to avoid compatibility issues
117 104
118 For tool-specific issues: 105 For tool-specific issues:
119 1. Check individual tool documentation 106 1. Check individual tool documentation
120 2. Review parameter requirements and formats 107 2. Review parameter requirements and formats
121 3. Test with smaller datasets first 108 3. Test with smaller datasets first
122 4. Consult [troubleshooting guide](../troubleshooting.md) 109 4. Consult [troubleshooting guide](/troubleshooting.md)
123 110
124 ## Contributing 111 ## Contributing
125 112
126 Help improve tool documentation: 113 Help improve tool documentation:
127 - Report unclear instructions 114 - Report unclear instructions