Biological network data tutorial
Author: Susan Steinbusch-Coort
Last updated 2023-09-21
In this skills session, you will learn:
- how to upload a biological network from STRING
- how to extend a network using CyTargetLinker
- how to load a pathway diagram from WikiPathways
- how to upload a network shared via NDEx
- how to visualize data in a network
- how to create a sub network
- how to extend a network via R
Preparation
- For the assignments you need to download and unpack the data for the two use cases
- Download UseCase1.zip from here
- Download UseCase2.zip from here
- Unpack both files
- In UseCase1 also unpack in directory LinkSets -> chembl_23_hsa_20180126.zip
Op Cytoscape and go to Apps -> App Manager and install the following Cytoscape apps:
- stringApp
- WikiPathways
- CyTargetLinker
- CyNDEx-2
Restart Cytoscape after installing the Apps.
Go through the following parts and answer the questions
- Part A: STRING
- Part B: WikiPathways
- Part C: NDEx
- Part D: Automation
- Part E: Application