Integrates multiscale community detection and functional enrichment for network analysis. CDAPS

Create a co-expression network between a subset of genes and all other genes of 1 or more species, grouping nodes by gene family.

ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.

Visualize CausalPath (causalpath.org) results in Cytoscape

identify differentially regulated sub-networks from gene expression data using known disease associations

Creates and visualizes a functionally grouped network of terms/pathways

Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.

Clusters a given network based on topology to find densely connected regions.

Import and augment Cytoscape networks from STRING

CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data

Highly sophisticated algorithms for arranging networks.