Basic stringApp tutorial: Cytoscape app store, STRING protein query, and omics data visualization
A basic bioinformatics tutorial on how to use Cytoscape and the Cytoscape stringApp. I first show how to install stringApp from the Cytoscape App Store, query STRING with a list of proteins via stringApp, and thereby retrieve a functional association network in Cytoscape. I then show how to import the omics data itself into the Cytoscape node table and finally use it to color the nodes in the network. I recommend that you watch my brief introductions to Cytoscape ( • The Cytoscape platform: Brief introduction... ) and stringApp ( • Cytoscape stringApp: Brief introduction to... ) before watching this tutorial. 0:00 Introduction: Cytoscape stringApp and overview of the tutorial 0:49 Installation: Cytoscape user interface, spreadsheet with omics data, and installing stringApp 1:40 Protein query: querying with a list of proteins and network retrieval 2:26 STRING panel: altering the look of the network through the STRING panel 2:58 Data tables: node table with protein information and edge table with STRING associations 3:17 Table import: correctly importing the omics spreadsheet into the node table 3:50 Data visualization: changing the visual style to color nodes based on imported data Hands-on exercises on Cytoscape stringApp are available at https://jensenlab.org/training/string...
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