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NetworkAnalyzer Frequently Asked Questions

General Questions

What is NetworkAnalyzer?

NetworkAnalyzer is a Java plugin for the Cytoscape platform. It performs analysis of biological networks and calculates network topology parameters including the diameter of a network, the average number of neighbors, and the number of connected pairs of nodes. It also computes the distributions of more complex network parameters such as node degrees, average clustering coefficients, topological coefficients, and shortest path lengths. It displays the results in charts, which can be saved as images or text files.

Where to find the online help page?

Definitions of the topological parameters computed by NetworkAnalyzer are available on this help page. You can also download the help page for offline reading here.

How to cite NetworkAnalyzer?

Please use the following reference to cite the use of NetworkAnalyzer in your work:

Assenov, Y., Ramírez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M.
Computing topological parameters of biological networks.
Bioinformatics, 2008, 24(2):282-284, 2008

How can I request new features or report a problem?

If you have encountered problems using NetworkAnalyzer or have suggestions for new features, please contact the Cytoscape development team directly using the Cytoscape Bug Tracker.

Who develops NetworkAnalyzer?

NetworkAnalyzer was initially developed by members of the Department of Computational Biology and Applied Algorithmics at the Max Planck Institute for Informatics, Saarbrücken, Germany.
NetworkAnalyzer is now a Cytoscape core plugin and maintained by the Cytoscape development team.

Requirements and Installation of NetworkAnalyzer

How to install NetworkAnalyzer?

Cytoscape versions 2.8 and newer include NetworkAnalyzer as core plugin.

If you are using Cytoscape 2.7, you can install NetworkAnalyzer through the plugin manager. You need to specify the following download site:
If you are not an experienced Cytoscape user, you can follow the step-by-step instructions on installing NetworkAnalyzer.

Can I run NetworkAnalyzer as a stand-alone application?

No, NetworkAnalyzer is a Java plugin for Cytoscape and does not run without it.

Network Parameters

How are the network parameters defined?

Please look at the online help of NetworkAnalyzer for definitions of the simple and complex network topology parameters. More information can be found in the articles referenced at the bottom of the help page.

You can also download the help page for offline reading.

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