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1 # Tutorials
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2
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3 Learn COBRAxy through hands-on tutorials for web-based analysis.
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5 To set up Galaxy and start using it for web-based analyses, see the [Galaxy Setup](tutorials/galaxy-setup)
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6
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7 ## Available Workflows
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8
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9 This is a collection of GALAXY workflows illustrating different applications of the tool.
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10 The general repository is at the following link: [Galaxy workflows](http://marea4galaxy.cloud.ba.infn.it/galaxy/workflows/list_published).
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11
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12 To use a workflow, click the "Import" button, and it will be added to your personal workflow page.
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13
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14 | Tutorial | Description | 🌐 Galaxy Workflow | 📘 Documentation |
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15 |-----------|-------------|--------------------|------------------|
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16 | **Flux Enrichment Analysis (Sampling Mean) — Separated Datasets** | Generate flux maps highlighting differences between two conditions. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=16e792953f5b45db) | [📄 See section](#flux-enrichment-analysis-sampling-mean--separated-datasets) |
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17 | **Flux Clustering (Sampling Mean) + Flux Enrichment Analysis** | Cluster fluxes and identify condition-specific differences. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=c851ab275e52f8af) | [📄 See section](#flux-clustering-sampling-mean--flux-enrichment-analysis) |
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18 | **Flux Enrichment Analysis (pFBA) — Separated Datasets** | Compare fluxes between two conditions using pFBA simulations. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=bf0806da5b28c6d9) | [📄 See section](#flux-enrichment-analysis-pfba--separated-datasets) |
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19 | **Flux Clustering (pFBA) + Flux Enrichment Analysis** | Cluster pFBA-derived fluxes and analyze enriched pathways. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=be0a27b9edd0db03) | [📄 See section](#flux-clustering-pfba--flux-enrichment-analysis) |
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20 | **RAS Clustering + Reaction Enrichment Analysis** | Cluster RAS profiles and identify significantly enriched reactions. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=81991b32733a4fc4) | [📄 See section](#ras-clustering--reaction-enrichment-analysis) |
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21 | **Reaction Enrichment Analysis — Unified Datasets** | Compare RAS profiles between classes within one dataset. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=0d16186aaff7cbfd) | [📄 See section](#reaction-enrichment-analysis--unified-datasets) |
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22 | **Reaction Enrichment Analysis — Separated Datasets** | Analyze RAS differences between two distinct datasets. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=290670ee50ab85f0) | [📄 See section](#reaction-enrichment-analysis--separated-datasets) |
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23
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24
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25 A more detailed description of the tools is available on the corresponding GALAXY page.
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26
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27 ### Flux Enrichment Analysis (Sampling Mean) — Separated Datasets
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28
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29 #### Goal
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30 Perform a **statistical analysis of fluxes** from two different datasets derived from flux simulations using the **sampling mean** method.
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31
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32 #### Scenario
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33 You have **one gene expression dataset per condition** (e.g., *Cancer vs Normal*).
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34
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35 #### 1. Import Metabolic Model
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36 - Load the metabolic model.
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37 - Define the **medium** and the **gene nomenclature format**.
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38
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39 #### 2. Expression to RAS
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40 - Transform a **gene expression file** into a **RAS dataset**.
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41 - This step must be applied **individually for each dataset**.
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42
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43 #### 3. RAS to Bounds
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44 - Use the **two RAS datasets** (one per condition) as input.
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45 - Generate the corresponding **flux bounds**.
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46
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47 #### 4. Flux Simulation
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48 - Use the **output from the RAS to Bounds** step as input.
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49 - Select **sampling mean (mean)** as the simulation method.
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50
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51 #### 5. Metabolic Flux Enrichment Analysis
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52 - Create a **map of significant differences** between fluxes from the two datasets.
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53 - Use the **flux simulation output** together with the **RASToBounds results** to identify enriched pathways or reactions.
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54
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55
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56 ### Flux Clustering (Sampling Mean) + Flux Enrichment Analysis
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57
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58 #### Goal
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59 Creation of **flux maps** from two different datasets and **clustering** based on flux simulations using the **sampling mean** method.
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60
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61 #### Scenario
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62 You have **one gene expression dataset**.
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63
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64 #### 1. Import Metabolic Model
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65 - Load the metabolic model.
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66 - Define the **medium** and the **gene nomenclature format**.
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67
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68 #### 2. Expression to RAS
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69 - Transform a **gene expression file** into a **RAS dataset**.
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70 - This step must be applied **for each dataset**.
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71
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72 #### 3. RAS to Bounds
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73 - Use **two different RAS datasets** as input.
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74 - Generate the corresponding **flux bounds**.
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75
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76 #### 4. Flux Simulation
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77 - Use the **output from the RAS to Bounds** step as input.
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78 - Select **sampling mean (mean)** as the simulation method.
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79
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80 #### 5. Cluster Analysis
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81 - Perform **clustering** on the **flux dataset** obtained from the simulation.
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82 - Identify patterns or groups within the flux profiles.
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83
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84 #### 6. Metabolic Flux Enrichment Analysis
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85 - Create **flux maps** showing **significant differences** between clusters.
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86 - Use:
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87 - The **clusters** as the *sample group specification*.
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88 - The **mean of each sample** from flux sampling as the *input flux data*.
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89
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90
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91 ### Flux Enrichment Analysis (pFBA) — Separated Datasets
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92
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93 #### Goal
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94 Perform a **statistical analysis of fluxes** from two different datasets obtained from flux simulations using **pFBA** (parsimonious Flux Balance Analysis).
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95
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96 #### Scenario
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97 You have **one gene expression dataset per condition** (e.g., *Cancer vs Normal*).
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98
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99 #### 1. Import Metabolic Model
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100 - Load the metabolic model.
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101 - Define the **medium** and the **gene nomenclature format**.
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102
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103 #### 2. Expression to RAS
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104 - Transform a **gene expression file** into a **RAS dataset**.
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105 - This step must be applied **individually for each dataset**.
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106
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107 #### 3. RAS to Bounds
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108 - Use the **two RAS datasets** (one per condition) as input.
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109 - Generate the corresponding **flux bounds**.
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110
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111 #### 4. Flux Simulation
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112 - Use the **output from the RAS to Bounds** step as input.
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113 - Select **pFBA** as the simulation method.
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114
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115 #### 5. Metabolic Flux Enrichment Analysis
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116 - Perform **analysis and visualization** of **significant differences** between fluxes of the two groups (e.g., *Normal* vs *Cancer*).
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117 - Use the **flux simulation output** together with the **RASToBounds results** to identify enriched or altered metabolic pathways.
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118
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119
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120 ### Flux Clustering (pFBA) + Flux Enrichment Analysis
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121
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122 #### Goal
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123 Perform a **statistical analysis of fluxes** from two datasets using **clusters derived from flux simulations** with **pFBA** (parsimonious Flux Balance Analysis).
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124
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125 #### Scenario
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126 You have **two gene expression datasets**.
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127
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128 #### 1. Import Metabolic Model
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129 - Load the metabolic model.
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130 - Define the **medium** and the **gene nomenclature format**.
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131
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132 #### 2. Expression to RAS
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133 - Transform each **gene expression file** into a **RAS dataset**.
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134 - This step must be applied **for each dataset**.
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135
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136 #### 3. RAS to Bounds
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137 - Use the **two RAS datasets** as input.
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138 - Generate the corresponding **flux bounds**.
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139
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140 #### 4. Flux Simulation
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141 - Use the **output from the RAS to Bounds** step as input.
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142 - Select **pFBA** as the simulation method.
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143
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144 #### 5. Cluster Analysis
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145 - Perform **clustering** on the **flux dataset** obtained from the pFBA simulation.
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146 - Identify clusters or groups within the flux profiles.
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147
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148 #### 6. Metabolic Flux Enrichment Analysis
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149 - Perform **analysis and visualization** of **significant differences** between fluxes of different clusters.
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150 - Use:
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151 - The **clusters** as the *sample group specification*.
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152 - The **output from the pFBA flux simulation** as the *input flux data*.
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153 - Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.
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154
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155
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156 ### RAS Clustering + Reaction Enrichment Analysis
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157
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158 #### Goal
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159 Perform **RAS statistical analysis** using the **MaREA** tool.
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160 Compare **RAS clusters** obtained from a **single gene expression dataset**.
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161
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162 #### Scenario
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163 You have **one gene expression dataset**.
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164
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165 #### 1. Import Metabolic Model
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166 - Load the metabolic model.
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167 - Define the **medium** and the **gene nomenclature format**.
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168
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169 #### 2. Expression to RAS
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170 - Transform the **gene expression file** into a **RAS dataset**.
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171
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172 #### 3. Cluster Analysis
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173 - Perform **clustering** on the **RAS dataset**.
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174 - Identify distinct clusters or groups within the data.
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175
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176 #### 4. Metabolic Reaction Enrichment Analysis (MaREA)
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177 - Perform **analysis and visualization** of **significant differences** between RAS values of different clusters.
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178 - Use **MaREA** to detect enriched reactions and metabolic changes.
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179 - Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.
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180
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181 ### Reaction Enrichment Analysis — Unified Datasets
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182
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183 #### Goal
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184 Perform **RAS statistical analysis** using the **MaREA** tool.
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185 Compare **groups within the same gene expression dataset**.
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186
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187 #### Scenario
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188 You have **one gene expression dataset** along with the **corresponding class labels** (e.g., *Normal* vs *Cancer*).
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189
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190 #### 1. Import Metabolic Model
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191 - Load the metabolic model.
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192 - Define the **medium** and the **gene nomenclature format**.
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193
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194 #### 2. Expression to RAS
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195 - Transform the **gene expression file** into a **RAS dataset**.
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196
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197 #### 3. Metabolic Reaction Enrichment Analysis (MaREA)
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198 - Perform **analysis and visualization** of **significant differences** between RAS values of different groups (e.g., *Normal* vs *Cancer*).
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199 - The **classes** are provided as input and used for **sample group specification** in the tool.
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200 - Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.
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201
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202 ### Reaction Enrichment Analysis — Separated Datasets
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203
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204 #### Goal
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205 Perform **RAS statistical analysis** using the **MaREA** tool with **different gene expression datasets**.
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206
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207 #### Scenario
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208 You have **one gene expression dataset per condition** (e.g., *Cancer* vs *Normal*).
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209
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210 #### 1. Import Metabolic Model
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211 - Load the metabolic model.
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212 - Define the **medium** and the **gene nomenclature format**.
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213
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214 #### 2. Expression to RAS
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215 - Transform each **gene expression file** into a **RAS dataset**.
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216 - This step must be applied **individually for each dataset**.
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217
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218 #### 3. Metabolic Reaction Enrichment Analysis (MaREA)
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219 - Perform **analysis and visualization** of **significant differences** between RAS values from two different datasets.
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220 - In this scenario, the **two RAS datasets** are provided as **separate inputs**.
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221 - Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.
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222
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223
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224 ## Tutorial Data
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225
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226 Download example datasets used in tutorials:
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227
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228 ```bash
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229 # Download tutorial data
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230 wget https://github.com/CompBtBs/COBRAxy/blob/main/data_tutorial/data_tutorial.zip
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231 unzip tutorial_data.zip
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232 ```
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233
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234 The tutorial data includes Sample gene expression datasets (Cancer.txt and Normal.txt)
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235
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236 ## Getting Help
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237
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238 If you encounter issues during tutorials:
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239
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240 1. Check the specific tutorial's troubleshooting section
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241 2. Refer to the main [Troubleshooting Guide](troubleshooting)
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242
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243 ## Contributing
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244
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245 Found an error or want to improve a tutorial?
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246
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247 - [Edit on GitHub](https://github.com/CompBtBs/COBRAxy/tree/main/docs/tutorials)
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248 - [Report issues](https://github.com/CompBtBs/COBRAxy/issues)
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249 - Suggest new tutorial topics
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250
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251 Ready to start? Pick your first tutorial above! 🚀
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