Man pages for stringgaussnet
PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor
| 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 |
| convertAliases | Convert aliases |
| convertToDistGraph | Convert to distance graph from STRINGNet |
| DEGeneExpr | Generic function for objects of class DEGeneExpr. |
| DEGeneExpr.default | Creation of DEGenesExpr object. |
| export | Generic function to export network objects from package... |
| export.ShortPathSTRINGNet | Export ShortPathSTRINGNet |
| export.SIMoNeNet | Export SIMoNeNet |
| export.STRINGNet | Export STRINGNet |
| export.WGCNANet | Export WGCNANet |
| FactorNetworks | Generic function for objects of class FactorNetworks |
| FactorNetworks.default | Function to create an object of class FactorNetworks |
| FilterEdges | Filter edges on network. |
| FilterEdges.FactorNetworks | Filter edges in FactorNetworks |
| FilterEdges.ShortPathSTRINGNet | Filter edges in ShortPathSTRINGNet |
| FilterEdges.SIMoNeNet | Filter edges in SIMoNeNet |
| findShortestPathways | Find shortest pathways between selected nodes |
| 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 |
| mapAttributes | Map attributes for toCytoscape() |
| mergeFactorEdges | Merge FactorNetworks edges |
| mergeGaussEdges | Merge gaussian networks edges |
| MultiDEGeneExpr | Generic function for objects of class MultiDEGeneExpr |
| MultiDEGeneExpr.default | Function to create an object of class MultiDEGeneExpr |
| MultiNetworks | Generic function for objects of class MultiNetworks |
| 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 |
| print.DEGeneExpr | Print function for object of class DEGeneExpr. |
| print.FactorNetworks | Print function for object of class FactorNetworks |
| print.MultiDEGeneExpr | Print function for object of class MultiDEGeneExpr |
| print.MultiNetworks | Print function for object of class MultiNetworks |
| print.ShortPathSTRINGNet | Print function for object of class ShortPathSTRINGNet. |
| print.SIMoNeNet | Print function for object of class SIMoNeNet. |
| print.STRINGNet | Print function for object of class STRINGNet. |
| print.WGCNANet | Print function for object of class WGCNANet. |
| resetCytoscapeSession | Reset Cytoscape session |
| saveCytoscapeSession | Save Cytoscape session |
| selectInteractionTypes | Select interaction sources in STRINGNet object |
| ShortPathSTRINGNet | Generic function for objects of class ShortPathSTRINGNet. |
| ShortPathSTRINGNet.default | Function to create object of class ShortPathSTRINGNet |
| SIMoNeNet | Generic function for objects of class SIMoNeNet |
| SIMoNeNet.default | Function to create object of class SIMoneNet |
| SpADataExpression | Data expression of the 75 DE genes identified by LIMMA in SpA... |
| SpADEGenes | 75 DE genes analysis results from LIMMA. |
| SpASamples | Samples description for SpA example data. |
| stringgaussnet-package | stringgaussnet |
| STRINGNet | Generic function for objects of class STRINGNet. |
| STRINGNet.default | Function to create an object of class STRINGNet |
| summary.ShortPathSTRINGNet | Summary function for object of class ShortPathSTRINGNet |
| summary.SIMoNeNet | Summary function for object of class SIMoNeNet |
| summary.STRINGNet | Summary function for object of class STRINGNet |
| summary.WGCNANet | Summary function for object of class WGCNANet |
| toCytoscape | Converts from igraph to Cytoscape object |
| WGCNANet | Generic function for objects of class WGCNANet |
| WGCNANet.default | Function to create an object of class WGCNANet |
