Calculates the network coherence of differentially expressed genes within a network.

an efficient app for hierarchical clustering and phylogenetics of complex networks

Orthoscape aimed to analyze evolutionary information in the gene networks and gene sets

Generate residue-to-residue connections provided by XL-MS in protein interaction networks

Import and augment Cytoscape networks from STRING

Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.

Creates and visualizes a functionally grouped network of terms/pathways

Import and augment Cytoscape networks from STRING

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

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

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

Highly sophisticated algorithms for arranging networks.