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 |