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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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4
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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 |
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15 |----------|-------------|
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16 |[Flux Enrichment Analysis - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=a64417ff266b740e) | Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
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17 | [Flux Enrichment Analysis (sampling mean) - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=16e792953f5b45db) | Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
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18 | [Flux clustering (sampling mean) + Flux Enrichment Analys](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=c851ab275e52f8af) | Creation of maps of the fluxes, using one dataset differently expressed for each condition and its sample group specification|
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19 | [Flux Enrichment Analysis (pFBA) - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=bf0806da5b28c6d9) | Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
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20 | [Flux clustering (pFBA) + Flux Enrichment Analysis](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=be0a27b9edd0db03) | Creation of maps of the fluxes, using one dataset differently expressed for each condition and its sample group specification |
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21 | [RAS clustering + Reaction Enrichment Analysis](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=81991b32733a4fc4) | Creation of RAS maps, one single expression gene dataset and its sample group specification |
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22 | [Reaction Enrichment Analysis - unified datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=0d16186aaff7cbfd) |Creation of RAS maps starting from an expression dataset and its corresponding classes. One gene expression dataset as input and its classes to compare. |
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23 | [Reaction Enrichment Analysis - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=290670ee50ab85f0) | Creation of RAS maps using the tool MaREA. Confrontation of two datasets that must be different from one another. |
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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 ## Tutorial Data
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28
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29 Download example datasets used in tutorials:
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30
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31 ```bash
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32 # Download tutorial data
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33 wget https://github.com/CompBtBs/COBRAxy/blob/main/data_tutorial/data_tutorial.zip
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34 unzip tutorial_data.zip
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35 ```
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37 The tutorial data includes Sample gene expression datasets (Cancer.txt and Normal.txt)
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38
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39 ## Getting Help
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40
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41 If you encounter issues during tutorials:
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42
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43 1. Check the specific tutorial's troubleshooting section
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44 2. Refer to the main [Troubleshooting Guide](troubleshooting)
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45
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46 ## Contributing
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47
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48 Found an error or want to improve a tutorial?
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49
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50 - [Edit on GitHub](https://github.com/CompBtBs/COBRAxy/tree/main/docs/tutorials)
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51 - [Report issues](https://github.com/CompBtBs/COBRAxy/issues)
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52 - Suggest new tutorial topics
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53
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54 Ready to start? Pick your first tutorial above! 🚀
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