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Functional module detection

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	ClueGO
	Creates and visualizes a functionally grouped network of terms/pathways

	ClueGO
	Creates and visualizes a functionally grouped network of terms/pathways
	(318) 404899 downloads

	DAPath
	Disease Associated Path Analyzer

	DAPath
	Disease Associated Path Analyzer
	(0) 5117 downloads

	jActiveModules
	Finds clusters where member nodes show significant changes in expression levels.

	jActiveModules
	Finds clusters where member nodes show significant changes in expression levels.
	(36) 67069 downloads

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

	PhenomeScape
	identify differentially regulated sub-networks from gene expression data using known disease associations
	(4) 15246 downloads

	SAFE
	Spatial Analysis for Functional Enrichment

	SAFE
	Spatial Analysis for Functional Enrichment
	(0) 8660 downloads

	ClustnSee 3
	clustering, module exploration and annotation

	ClustnSee 3
	clustering, module exploration and annotation
	(1) 1478 downloads

	iRegulon
	Detects master regulators and cis-regulatory interactions

	iRegulon
	Detects master regulators and cis-regulatory interactions
	(12) 39422 downloads

	PEPPER
	Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization

	PEPPER
	Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
	(44) 32378 downloads

	ReactomeFIPlugIn
	Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network

	ReactomeFIPlugIn
	Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
	(23) 141264 downloads