PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor


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Documentation for package ‘stringgaussnet’ version 1.1

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stringgaussnet-package stringgaussnet
addFactorGraphsToCytoscape Add FactorNetworks object to Cytoscape
addGraphToCytoscape Add network to Cytoscape
addMultiGraphToCytoscape Add MultiNetworks to Cytoscape
addNetworkStyle Add network style to Cytoscape
addShortPathSTRINGNetMappings Add Cytoscape mapping for ShortPathSTRINGNet
addSIMoNeNetMappings Add Cytoscape mapping for SIMoNeNet
addSkeletonDefaults Add default values for Cytoscape styles
addSkeletonMappings Add default mappings for Cytoscape styles
addSTRINGNetMappings Add Cytoscape mapping for STRINGNet
addWGCNANetMappings Add Cytoscape mapping for WGCNANet
applyLayout Apply layout to a network in Cytoscape
applyStyle Apply style to a network in Cytoscape
as.igraph.stringgaussnet Convert stringgaussnet network into igraph
checkCytoscapeRunning Check Cytoscape running
compareFactorNetworks Compare levels of FactorNetworks
compareGaussNetworks Compare gaussian networks
computeCombinedScores Compute STRING combined scores
computeSimilarities Compute similarities for WGCNA
convertToDistGraph Convert to distance graph from STRINGNet
DEGeneExpr.default Creation of DEGenesExpr object.
export.ShortPathSTRINGNet Export ShortPathSTRINGNet
export.SIMoNeNet Export SIMoNeNet
export.STRINGNet Export STRINGNet
export.WGCNANet Export WGCNANet
FactorNetworks.default Function to create an object of class FactorNetworks
FilterEdges.FactorNetworks Filter edges in FactorNetworks
FilterEdges.ShortPathSTRINGNet Filter edges in ShortPathSTRINGNet
FilterEdges.SIMoNeNet Filter edges in SIMoNeNet
getGenesInformations Get gene annotations
getMartDatasets Gert maRt datasets
getShortestPaths Get shortest paths between given nodes in STRING network.
getSIMoNeNet Infer SIMoNe network from expression data
getSTRINGNet Get STRING network from gene identifiers
getWGCNANet Infer WGCNA network from expression data
MultiDEGeneExpr.default Function to create an object of class MultiDEGeneExpr
MultiNetworks.default Function to create an object of class MultiNetworks
pickSIMoNeParam Pick SIMoNe parameters
pickWGCNAParam Pick WGCNA parameters
plot.FactorNetworks Plot FactorNetworks
plot.SIMoNeNet Plot SIMoNeNet
plot.WGCNANet Plot WGCNANet
resetCytoscapeSession Reset Cytoscape session
saveCytoscapeSession Save Cytoscape session
selectInteractionTypes Select interaction sources in STRINGNet object
ShortPathSTRINGNet.default Function to create object of class ShortPathSTRINGNet
SIMoNeNet.default Function to create object of class SIMoneNet
stringgaussnet stringgaussnet
STRINGNet.default Function to create an object of class STRINGNet
WGCNANet.default Function to create an object of class WGCNANet