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This page has been deprecated and is no longer updated. The current version of the Cytoscape manual can be found at http://manual.cytoscape.org/

What are apps?

Cytoscape's capabilities are not fixed. They can be expanded with apps. They can extend Cytoscape in a variety of ways. One app can have the ability to import data from an online database. Another app could provide a new method for analyzing networks. You can install apps after you have installed Cytoscape. Most apps were made by Cytoscape users like you.

If you're familiar with Cytoscape 2.x, you probably know that Cytoscape apps were called plugins. Starting in Cytoscape 3.0, we are calling them apps. Cytoscape 2.x plugins cannot be used in Cytoscape 3.0.

Installing Apps

You can install apps through the App Store or within Cytoscape. In this section, we'll talk about installing apps through Cytoscape. You can learn how to install apps through the App Store here.

To install apps within Cytoscape, go to the menu bar and choose Apps → App Manager. At the top of the App Manager window, make sure you have the Install tab selected.

There are three ways you can find apps:

When you click on an app in the middle panel, the App Manager shows its short description and icon in the right panel. If you want more information about the app, click the View on App Store button on the bottom-right. If you want to go ahead and install the app, click the Install button.

If you've downloaded an app to your computer, you can install it by clicking the Install from File button on the bottom-left.

Managing your Installed Apps

You can see a list of all apps you have installed by clicking the Currently Installed tab at the top. When you click on an app in the list, you'll see a description of your app at the bottom. At the bottom, you'll see a couple buttons where you can:

Cytoscape_3/UserManual/AppManager (last edited 2016-04-26 22:18:24 by TimHull)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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