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. |
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. |
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: |
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. |