Ontology analysis

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

Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation

Finds candidate genes in a network that are associated with user-defined target GO terms.

A WikiData explorer for Cytoscape

Creates and visualizes a functionally grouped network of terms/pathways

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

Analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity

a tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization

Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.

Finds enriched function based on sum-of-weight scores.

Systematically partition the given graph, and layout and color nodes based on GO terms.

Builds a network in Cytoscape from a user-provided OWL/RDF ontology and it implements a SPARQL module

Assesses similarity of gene ontologies for given genes and their neighbours. All files must be installed in plugin folder.

Visualizes networks by semantic similarities.

The Network Ontology Analysis plugin performs ontology overrepresentation analysis based on the network connections among annotate nodes.

Allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.

Statistical Tracking of Ontological Phrases