Help:DataVisualizationInCytoscape
From WikiPathways
(Difference between revisions)
| Line 18: | Line 18: | ||
[http://apps.cytoscape.org/apps/bridgedb BridgeDb app] | [http://apps.cytoscape.org/apps/bridgedb BridgeDb app] | ||
| - | == Download and prepare tutorial data == | + | === Download and prepare tutorial data === |
| - | + | For this tutorial, we will use an example dataset of transcriptional profiling of mouse embryonic stem cells and embryoid bodies. The data is in the form of a text file. | |
| - | The data | + | The experimental data for this tutorial can be found here: [http://opentutorials.cgl.ucsf.edu/index.php/File:MusMusculus_ES-EB_25000.txt]. |
= Importing and mapping data = | = Importing and mapping data = | ||
| - | == Data import == | + | === Data import === |
| - | == Identifier mapping with BridgeDb == | + | === Identifier mapping with BridgeDb === |
= Viewing data on pathways = | = Viewing data on pathways = | ||
| - | == Open WikiPathways in Cytoscape == | + | === Open WikiPathways in Cytoscape === |
| - | == Visual Styles == | + | === Visual Styles === |
Revision as of 18:47, 6 January 2016
UNDER CONSTRUCTION
Contents |
Installation
Cytoscape
- Download Cytoscape here: http://www.cytoscape.org/.
- Launch Cytoscape
WikiPathways Apps
- In Cytoscape, open the App Manager under Apps > App Manager.
- In the Search field, type WikiPathways to search for the WikiPathways app. In the search results, select the WikiPathways app and click Install.
- Next, find and install the BridgeDb app in the same way. When the installation is complete, click Close to exit the App Manager.
Alternatively, Cytoscape apps can be installed directly from the Cytoscape App Store. If Cytoscape is open on your computer, you can click Install on the relevant app page, and the app will install.
Download and prepare tutorial data
For this tutorial, we will use an example dataset of transcriptional profiling of mouse embryonic stem cells and embryoid bodies. The data is in the form of a text file.
The experimental data for this tutorial can be found here: [1].
