stringgaussnet: PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor
Version 1.1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("stringgaussnet")

Getting started

Package overview
Stringgaussnet: user''s guide

Popular man pages

addGraphToCytoscape: Add network to Cytoscape
addMultiGraphToCytoscape: Add MultiNetworks to Cytoscape
addNetworkStyle: Add network style to Cytoscape
applyLayout: Apply layout to a network in Cytoscape
getSTRINGNet: Get STRING network from gene identifiers
mapAttributes: Map attributes for toCytoscape()
toCytoscape: Converts from igraph to Cytoscape object
See all...

All man pages Function index File listing

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

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

Files

inst
inst/doc
inst/doc/stringgaussnet.R
inst/doc/stringgaussnet.pdf
inst/doc/stringgaussnet.Rmd
NAMESPACE
data
data/SpADEGenes.rda
data/SpASamples.rda
data/SpADataExpression.rda
R
R/WGCNANet.R
R/STRINGNet.R
R/checkCytoscapeRunning.R
R/getMartDatasets.R
R/MultiNetworks.R
R/DEGeneExpr.R
R/addFactorGraphsToCytoscape.R
R/print.STRINGNet.R
R/FactorNetworks.R
R/export.SIMoNeNet.R
R/print.FactorNetworks.R
R/plot.WGCNANet.R
R/ShortPathSTRINGNet.R
R/mapAttributes.R
R/resetCytoscapeSession.R
R/MultiDEGeneExpr.default.R
R/SIMoNeNet.R
R/addGraphToCytoscape.R
R/convertAliases.R
R/summary.SIMoNeNet.R
R/summary.WGCNANet.R
R/SIMoNeNet.default.R
R/export.ShortPathSTRINGNet.R
R/addNetworkStyle.R
R/FilterEdges.ShortPathSTRINGNet.R
R/mergeFactorEdges.R
R/print.ShortPathSTRINGNet.R
R/computeSimilarities.R
R/plot.FactorNetworks.R
R/pickSIMoNeParam.R
R/toCytoscape.R
R/MultiDEGeneExpr.R
R/addSkeletonMappings.R
R/STRINGNet.default.R
R/getShortestPaths.R
R/export.WGCNANet.R
R/FilterEdges.SIMoNeNet.R
R/getWGCNANet.R
R/addMultiGraphToCytoscape.R
R/addSTRINGNetMappings.R
R/ShortPathSTRINGNet.default.R
R/getSIMoNeNet.R
R/plot.SIMoNeNet.R
R/FactorNetworks.default.R
R/print.WGCNANet.R
R/findShortestPathways.R
R/getSTRINGNet.R
R/summary.ShortPathSTRINGNet.R
R/print.MultiNetworks.R
R/addWGCNANetMappings.R
R/saveCytoscapeSession.R
R/FilterEdges.FactorNetworks.R
R/print.MultiDEGeneExpr.R
R/summary.STRINGNet.R
R/print.DEGeneExpr.R
R/export.R
R/DEGeneExpr.default.R
R/export.STRINGNet.R
R/getGenesInformations.R
R/applyLayout.R
R/convertToDistGraph.R
R/pickWGCNAParam.R
R/as.igraph.stringgaussnet.R
R/compareFactorNetworks.R
R/addSkeletonDefaults.R
R/selectInteractionTypes.R
R/applyStyle.R
R/MultiNetworks.default.R
R/print.SIMoNeNet.R
R/computeCombinedScores.R
R/addSIMoNeNetMappings.R
R/addShortPathSTRINGNetMappings.R
R/FilterEdges.R
R/WGCNANet.default.R
R/mergeGaussEdges.R
R/compareGaussNetworks.R
vignettes
vignettes/misc
vignettes/misc/Figure_pickWGCNA.png
vignettes/misc/bibliography.bib
vignettes/misc/Figure_ShortPathNetworks.png
vignettes/misc/Figure_FactorNetworks.png
vignettes/misc/Figure_CompareNetworks.png
vignettes/misc/Figure_Vignette.png
vignettes/stringgaussnet.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/print.MultiDEGeneExpr.Rd
man/plot.WGCNANet.Rd
man/MultiNetworks.Rd
man/getWGCNANet.Rd
man/STRINGNet.default.Rd
man/FactorNetworks.Rd
man/toCytoscape.Rd
man/checkCytoscapeRunning.Rd
man/MultiNetworks.default.Rd
man/SpADEGenes.Rd
man/export.STRINGNet.Rd
man/compareGaussNetworks.Rd
man/addNetworkStyle.Rd
man/DEGeneExpr.Rd
man/summary.WGCNANet.Rd
man/FilterEdges.FactorNetworks.Rd
man/print.FactorNetworks.Rd
man/convertAliases.Rd
man/stringgaussnet-package.Rd
man/computeSimilarities.Rd
man/FilterEdges.ShortPathSTRINGNet.Rd
man/addGraphToCytoscape.Rd
man/STRINGNet.Rd
man/addSIMoNeNetMappings.Rd
man/addShortPathSTRINGNetMappings.Rd
man/export.Rd
man/selectInteractionTypes.Rd
man/ShortPathSTRINGNet.default.Rd
man/compareFactorNetworks.Rd
man/getSIMoNeNet.Rd
man/mergeGaussEdges.Rd
man/export.ShortPathSTRINGNet.Rd
man/pickWGCNAParam.Rd
man/MultiDEGeneExpr.default.Rd
man/applyLayout.Rd
man/as.igraph.stringgaussnet.Rd
man/summary.SIMoNeNet.Rd
man/getMartDatasets.Rd
man/addMultiGraphToCytoscape.Rd
man/mergeFactorEdges.Rd
man/applyStyle.Rd
man/FilterEdges.Rd
man/convertToDistGraph.Rd
man/export.WGCNANet.Rd
man/plot.FactorNetworks.Rd
man/FactorNetworks.default.Rd
man/SIMoNeNet.default.Rd
man/SpASamples.Rd
man/SIMoNeNet.Rd
man/addWGCNANetMappings.Rd
man/WGCNANet.default.Rd
man/addFactorGraphsToCytoscape.Rd
man/getShortestPaths.Rd
man/getSTRINGNet.Rd
man/addSkeletonMappings.Rd
man/print.WGCNANet.Rd
man/summary.STRINGNet.Rd
man/addSkeletonDefaults.Rd
man/SpADataExpression.Rd
man/print.SIMoNeNet.Rd
man/pickSIMoNeParam.Rd
man/print.ShortPathSTRINGNet.Rd
man/addSTRINGNetMappings.Rd
man/getGenesInformations.Rd
man/DEGeneExpr.default.Rd
man/export.SIMoNeNet.Rd
man/print.DEGeneExpr.Rd
man/ShortPathSTRINGNet.Rd
man/mapAttributes.Rd
man/computeCombinedScores.Rd
man/MultiDEGeneExpr.Rd
man/saveCytoscapeSession.Rd
man/findShortestPathways.Rd
man/WGCNANet.Rd
man/FilterEdges.SIMoNeNet.Rd
man/print.MultiNetworks.Rd
man/summary.ShortPathSTRINGNet.Rd
man/print.STRINGNet.Rd
man/resetCytoscapeSession.Rd
man/plot.SIMoNeNet.Rd
stringgaussnet documentation built on May 19, 2017, 7:55 a.m.

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