The NDEx Project provides an open-source framework where scientists and organizations can store, share and publish biological network knowledge.
NDEx is fully integrated with the Cytoscape desktop application.
One simple query finds pathways, extracts neighborhoods from large protein interaction networks and discovers disease, drug, and other associations.
Powered by NDEx and integrated with Cytoscape.
Cytoscape is an open source software platform for visualizing complex networks and integrating these with attribute data.Read More
Browse and download hundreds of applications to extend Cytoscape's capabilities and features.Read More
Cytoscape tutorials and other training material including automation, data visualization and network analysis.Read More
UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments.
EMAP Toolbox is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
MiST: Mass Spectrometry interaction STatistics is a computational tool for scoring of affinity purification-mass spectrometry data. We have also developed a stand-alone version of MiST in R.Read more
The Clique Extracted Ontologies algorithm (CliXO) infers an ontology in the form of a hierarchical, directed acyclic graph (DAG) from pairwise similarity data. Originally developed for inferring gene ontologies from biological gene networks.
NeXO (The Network Extracted Ontology) is a gene ontology inferred directly from large-scale molecular networks. NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a complete hierarchy of cellular components and processes.Read more
NBS is a method for stratification (clustering) of patients within a cancer cohort based on genome scale somatic mutation measurements and a gene interaction network.