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

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.

AuthorEmmanuel Chaplais, Henri-Jean Garchon
Date of publication2015-07-22 12:18:19
MaintainerEmmanuel Chaplais <emmanuel.chaplais@inserm.fr>
LicenseGPL-3
Version1.1

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

Functions

addFactorGraphsToCytoscape Man page
addGraphToCytoscape Man page
addMultiGraphToCytoscape Man page
addNetworkStyle Man page
addShortPathSTRINGNetMappings Man page
addSIMoNeNetMappings Man page
addSkeletonDefaults Man page
addSkeletonMappings Man page
addSTRINGNetMappings Man page
addWGCNANetMappings Man page
applyLayout Man page
applyStyle Man page
as.igraph.stringgaussnet Man page
checkCytoscapeRunning Man page
compareFactorNetworks Man page
compareGaussNetworks Man page
computeCombinedScores Man page
computeSimilarities Man page
convertAliases Man page
convertToDistGraph Man page
DEGeneExpr Man page
DEGeneExpr.default Man page
export Man page
export.ShortPathSTRINGNet Man page
export.SIMoNeNet Man page
export.STRINGNet Man page
export.WGCNANet Man page
FactorNetworks Man page
FactorNetworks.default Man page
FilterEdges Man page
FilterEdges.FactorNetworks Man page
FilterEdges.ShortPathSTRINGNet Man page
FilterEdges.SIMoNeNet Man page
findShortestPathways Man page
getGenesInformations Man page
getMartDatasets Man page
getShortestPaths Man page
getSIMoNeNet Man page
getSTRINGNet Man page
getWGCNANet Man page
mapAttributes Man page
mergeFactorEdges Man page
mergeGaussEdges Man page
MultiDEGeneExpr Man page
MultiDEGeneExpr.default Man page
MultiNetworks Man page
MultiNetworks.default Man page
pickSIMoNeParam Man page
pickWGCNAParam Man page
plot.FactorNetworks Man page
plot.SIMoNeNet Man page
plot.WGCNANet Man page
print.DEGeneExpr Man page
print.FactorNetworks Man page
print.MultiDEGeneExpr Man page
print.MultiNetworks Man page
print.ShortPathSTRINGNet Man page
print.SIMoNeNet Man page
print.STRINGNet Man page
print.WGCNANet Man page
resetCytoscapeSession Man page
saveCytoscapeSession Man page
selectInteractionTypes Man page
ShortPathSTRINGNet Man page
ShortPathSTRINGNet.default Man page
SIMoNeNet Man page
SIMoNeNet.default Man page
SpADataExpression Man page
SpADEGenes Man page
SpASamples Man page
stringgaussnet Man page
stringgaussnet-package Man page
STRINGNet Man page
STRINGNet.default Man page
summary.ShortPathSTRINGNet Man page
summary.SIMoNeNet Man page
summary.STRINGNet Man page
summary.WGCNANet Man page
toCytoscape Man page
WGCNANet Man page
WGCNANet.default Man page

Files

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

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