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

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A toolbox for a construction of protein-protein interaction networks through the 'STRING' application programming interface, and an inference of Gaussian networks through 'SIMoNe' and 'WGCNA' approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active 'Cytoscape' session.

Author
Emmanuel Chaplais, Henri-Jean Garchon
Date of publication
2015-07-22 12:18:19
Maintainer
Emmanuel Chaplais <emmanuel.chaplais@inserm.fr>
License
GPL-3
Version
1.1

View on CRAN

Man pages

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

Files in this package

stringgaussnet
stringgaussnet/inst
stringgaussnet/inst/doc
stringgaussnet/inst/doc/stringgaussnet.R
stringgaussnet/inst/doc/stringgaussnet.pdf
stringgaussnet/inst/doc/stringgaussnet.Rmd
stringgaussnet/NAMESPACE
stringgaussnet/data
stringgaussnet/data/SpADEGenes.rda
stringgaussnet/data/SpASamples.rda
stringgaussnet/data/SpADataExpression.rda
stringgaussnet/R
stringgaussnet/R/WGCNANet.R
stringgaussnet/R/STRINGNet.R
stringgaussnet/R/checkCytoscapeRunning.R
stringgaussnet/R/getMartDatasets.R
stringgaussnet/R/MultiNetworks.R
stringgaussnet/R/DEGeneExpr.R
stringgaussnet/R/addFactorGraphsToCytoscape.R
stringgaussnet/R/print.STRINGNet.R
stringgaussnet/R/FactorNetworks.R
stringgaussnet/R/export.SIMoNeNet.R
stringgaussnet/R/print.FactorNetworks.R
stringgaussnet/R/plot.WGCNANet.R
stringgaussnet/R/ShortPathSTRINGNet.R
stringgaussnet/R/mapAttributes.R
stringgaussnet/R/resetCytoscapeSession.R
stringgaussnet/R/MultiDEGeneExpr.default.R
stringgaussnet/R/SIMoNeNet.R
stringgaussnet/R/addGraphToCytoscape.R
stringgaussnet/R/convertAliases.R
stringgaussnet/R/summary.SIMoNeNet.R
stringgaussnet/R/summary.WGCNANet.R
stringgaussnet/R/SIMoNeNet.default.R
stringgaussnet/R/export.ShortPathSTRINGNet.R
stringgaussnet/R/addNetworkStyle.R
stringgaussnet/R/FilterEdges.ShortPathSTRINGNet.R
stringgaussnet/R/mergeFactorEdges.R
stringgaussnet/R/print.ShortPathSTRINGNet.R
stringgaussnet/R/computeSimilarities.R
stringgaussnet/R/plot.FactorNetworks.R
stringgaussnet/R/pickSIMoNeParam.R
stringgaussnet/R/toCytoscape.R
stringgaussnet/R/MultiDEGeneExpr.R
stringgaussnet/R/addSkeletonMappings.R
stringgaussnet/R/STRINGNet.default.R
stringgaussnet/R/getShortestPaths.R
stringgaussnet/R/export.WGCNANet.R
stringgaussnet/R/FilterEdges.SIMoNeNet.R
stringgaussnet/R/getWGCNANet.R
stringgaussnet/R/addMultiGraphToCytoscape.R
stringgaussnet/R/addSTRINGNetMappings.R
stringgaussnet/R/ShortPathSTRINGNet.default.R
stringgaussnet/R/getSIMoNeNet.R
stringgaussnet/R/plot.SIMoNeNet.R
stringgaussnet/R/FactorNetworks.default.R
stringgaussnet/R/print.WGCNANet.R
stringgaussnet/R/findShortestPathways.R
stringgaussnet/R/getSTRINGNet.R
stringgaussnet/R/summary.ShortPathSTRINGNet.R
stringgaussnet/R/print.MultiNetworks.R
stringgaussnet/R/addWGCNANetMappings.R
stringgaussnet/R/saveCytoscapeSession.R
stringgaussnet/R/FilterEdges.FactorNetworks.R
stringgaussnet/R/print.MultiDEGeneExpr.R
stringgaussnet/R/summary.STRINGNet.R
stringgaussnet/R/print.DEGeneExpr.R
stringgaussnet/R/export.R
stringgaussnet/R/DEGeneExpr.default.R
stringgaussnet/R/export.STRINGNet.R
stringgaussnet/R/getGenesInformations.R
stringgaussnet/R/applyLayout.R
stringgaussnet/R/convertToDistGraph.R
stringgaussnet/R/pickWGCNAParam.R
stringgaussnet/R/as.igraph.stringgaussnet.R
stringgaussnet/R/compareFactorNetworks.R
stringgaussnet/R/addSkeletonDefaults.R
stringgaussnet/R/selectInteractionTypes.R
stringgaussnet/R/applyStyle.R
stringgaussnet/R/MultiNetworks.default.R
stringgaussnet/R/print.SIMoNeNet.R
stringgaussnet/R/computeCombinedScores.R
stringgaussnet/R/addSIMoNeNetMappings.R
stringgaussnet/R/addShortPathSTRINGNetMappings.R
stringgaussnet/R/FilterEdges.R
stringgaussnet/R/WGCNANet.default.R
stringgaussnet/R/mergeGaussEdges.R
stringgaussnet/R/compareGaussNetworks.R
stringgaussnet/vignettes
stringgaussnet/vignettes/misc
stringgaussnet/vignettes/misc/Figure_pickWGCNA.png
stringgaussnet/vignettes/misc/bibliography.bib
stringgaussnet/vignettes/misc/Figure_ShortPathNetworks.png
stringgaussnet/vignettes/misc/Figure_FactorNetworks.png
stringgaussnet/vignettes/misc/Figure_CompareNetworks.png
stringgaussnet/vignettes/misc/Figure_Vignette.png
stringgaussnet/vignettes/stringgaussnet.Rmd
stringgaussnet/MD5
stringgaussnet/build
stringgaussnet/build/vignette.rds
stringgaussnet/DESCRIPTION
stringgaussnet/man
stringgaussnet/man/print.MultiDEGeneExpr.Rd
stringgaussnet/man/plot.WGCNANet.Rd
stringgaussnet/man/MultiNetworks.Rd
stringgaussnet/man/getWGCNANet.Rd
stringgaussnet/man/STRINGNet.default.Rd
stringgaussnet/man/FactorNetworks.Rd
stringgaussnet/man/toCytoscape.Rd
stringgaussnet/man/checkCytoscapeRunning.Rd
stringgaussnet/man/MultiNetworks.default.Rd
stringgaussnet/man/SpADEGenes.Rd
stringgaussnet/man/export.STRINGNet.Rd
stringgaussnet/man/compareGaussNetworks.Rd
stringgaussnet/man/addNetworkStyle.Rd
stringgaussnet/man/DEGeneExpr.Rd
stringgaussnet/man/summary.WGCNANet.Rd
stringgaussnet/man/FilterEdges.FactorNetworks.Rd
stringgaussnet/man/print.FactorNetworks.Rd
stringgaussnet/man/convertAliases.Rd
stringgaussnet/man/stringgaussnet-package.Rd
stringgaussnet/man/computeSimilarities.Rd
stringgaussnet/man/FilterEdges.ShortPathSTRINGNet.Rd
stringgaussnet/man/addGraphToCytoscape.Rd
stringgaussnet/man/STRINGNet.Rd
stringgaussnet/man/addSIMoNeNetMappings.Rd
stringgaussnet/man/addShortPathSTRINGNetMappings.Rd
stringgaussnet/man/export.Rd
stringgaussnet/man/selectInteractionTypes.Rd
stringgaussnet/man/ShortPathSTRINGNet.default.Rd
stringgaussnet/man/compareFactorNetworks.Rd
stringgaussnet/man/getSIMoNeNet.Rd
stringgaussnet/man/mergeGaussEdges.Rd
stringgaussnet/man/export.ShortPathSTRINGNet.Rd
stringgaussnet/man/pickWGCNAParam.Rd
stringgaussnet/man/MultiDEGeneExpr.default.Rd
stringgaussnet/man/applyLayout.Rd
stringgaussnet/man/as.igraph.stringgaussnet.Rd
stringgaussnet/man/summary.SIMoNeNet.Rd
stringgaussnet/man/getMartDatasets.Rd
stringgaussnet/man/addMultiGraphToCytoscape.Rd
stringgaussnet/man/mergeFactorEdges.Rd
stringgaussnet/man/applyStyle.Rd
stringgaussnet/man/FilterEdges.Rd
stringgaussnet/man/convertToDistGraph.Rd
stringgaussnet/man/export.WGCNANet.Rd
stringgaussnet/man/plot.FactorNetworks.Rd
stringgaussnet/man/FactorNetworks.default.Rd
stringgaussnet/man/SIMoNeNet.default.Rd
stringgaussnet/man/SpASamples.Rd
stringgaussnet/man/SIMoNeNet.Rd
stringgaussnet/man/addWGCNANetMappings.Rd
stringgaussnet/man/WGCNANet.default.Rd
stringgaussnet/man/addFactorGraphsToCytoscape.Rd
stringgaussnet/man/getShortestPaths.Rd
stringgaussnet/man/getSTRINGNet.Rd
stringgaussnet/man/addSkeletonMappings.Rd
stringgaussnet/man/print.WGCNANet.Rd
stringgaussnet/man/summary.STRINGNet.Rd
stringgaussnet/man/addSkeletonDefaults.Rd
stringgaussnet/man/SpADataExpression.Rd
stringgaussnet/man/print.SIMoNeNet.Rd
stringgaussnet/man/pickSIMoNeParam.Rd
stringgaussnet/man/print.ShortPathSTRINGNet.Rd
stringgaussnet/man/addSTRINGNetMappings.Rd
stringgaussnet/man/getGenesInformations.Rd
stringgaussnet/man/DEGeneExpr.default.Rd
stringgaussnet/man/export.SIMoNeNet.Rd
stringgaussnet/man/print.DEGeneExpr.Rd
stringgaussnet/man/ShortPathSTRINGNet.Rd
stringgaussnet/man/mapAttributes.Rd
stringgaussnet/man/computeCombinedScores.Rd
stringgaussnet/man/MultiDEGeneExpr.Rd
stringgaussnet/man/saveCytoscapeSession.Rd
stringgaussnet/man/findShortestPathways.Rd
stringgaussnet/man/WGCNANet.Rd
stringgaussnet/man/FilterEdges.SIMoNeNet.Rd
stringgaussnet/man/print.MultiNetworks.Rd
stringgaussnet/man/summary.ShortPathSTRINGNet.Rd
stringgaussnet/man/print.STRINGNet.Rd
stringgaussnet/man/resetCytoscapeSession.Rd
stringgaussnet/man/plot.SIMoNeNet.Rd