NetworkAnalyzer

NetworkAnalyzer is a Java plugin for Cytoscape, a software platform for the analysis and visualization of molecular interaction networks. The plugin computes specific parameters describing the network topology. A typical analysis workflow using NetworkAnalyzer is described in this Nature Protocol.

Definitions of the parameters listed below are available on our help page. You can also download the help page for offline reading.

Feature List

The most comprehensive set of simple topological parameters
- Clustering coefficient
- Number of connected components
- Diameter and radius
- Centralization
- Number of shortest paths
- Average shortest path length
- Average number of neighbors
- Density
- Heterogeneity ^U
- Number of isolated nodes
- Number of self-loops
- Number of multi-edge node pairs
The most comprehensive set of complex topological parameters
- Degree distribution ^U
- In-degree distribution ^D
- Out-degree distribution ^D
- Average clustering coefficient distribution
- Shortest path length distribution
- Topological coefficients ^U
- Shared neighbors distribution ^U
- Neighborhood connectivity distribution ^U
- Neighborhood connectivity distribution (only in) ^D
- Neighborhood connectivity distribution (only out) ^D
- Neighborhood connectivity distribution (in and out) ^D
- Betweenness centrality vs. Number of neighbors
- Closeness centrality vs. Number of neighbors
- Stress centrality distribution
Batch analysis of multiple networks
Fitting a line and a power law
Visualizing correlation between two complex parameters
Saving and loading analysis results
Saving chart as an image file (PNG, JPEG or SVG)
Exporting complex parameter data to text file
Computing union, intersection and difference of two networks, extracting connected components and more
Mapping computed parameters to visual styles
Adjusting visual properties of the charts: title, axis labels, and more

^U Computed for undirected networks only.
^D Computed for directed networks only.

We have made a step-by-step tutorial on how to use NetworkAnalyzer for spotting hub nodes in a network.

To request another feature, please write an e-mail to Mario Albrecht.