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NDEx

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.

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NDEx IQuery

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.

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27 September 2021

- CURRENT PROTOCOLS -
NDEx: Accessing Network Models and Streamlining Network Biology Workflows.

Rudolf T. Pillich, Jing Chen,

et al.

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cytoscape

Cytoscape is an open source software platform for visualizing complex networks and integrating these with attribute data.

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APP STORE

Browse and download hundreds of applications to extend Cytoscape's capabilities and features.

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TUTORIALS

Cytoscape tutorials and other training material including automation, data visualization and network analysis.

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UCSF CHIMERA

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

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

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.

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CLIXO

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.

N<EXO

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.​

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Network based stratification (NBS)

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.

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