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stringgaussnet (version 1.1)

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

Description

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.

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Version

Install

install.packages('stringgaussnet')

Monthly Downloads

10

Version

1.1

License

GPL-3

Maintainer

Emmanuel Chaplais

Last Published

July 22nd, 2015

Functions in stringgaussnet (1.1)

stringgaussnet-package

stringgaussnet
DEGeneExpr.default

Creation of DEGenesExpr object.
FilterEdges.FactorNetworks

Filter edges in FactorNetworks
getSTRINGNet

Get STRING network from gene identifiers
FilterEdges

Filter edges on network.
addSIMoNeNetMappings

Add Cytoscape mapping for SIMoNeNet
as.igraph.stringgaussnet

Convert stringgaussnet network into igraph
addFactorGraphsToCytoscape

Add FactorNetworks object to Cytoscape
SIMoNeNet.default

Function to create object of class SIMoneNet
SpADEGenes

75 DE genes analysis results from LIMMA.
SpASamples

Samples description for SpA example data.
DEGeneExpr

Generic function for objects of class DEGeneExpr.
summary.ShortPathSTRINGNet

Summary function for object of class ShortPathSTRINGNet
print.ShortPathSTRINGNet

Print function for object of class ShortPathSTRINGNet.
convertAliases

Convert aliases
FilterEdges.SIMoNeNet

Filter edges in SIMoNeNet
export.WGCNANet

Export WGCNANet
MultiNetworks.default

Function to create an object of class MultiNetworks
FactorNetworks.default

Function to create an object of class FactorNetworks
addNetworkStyle

Add network style to Cytoscape
WGCNANet.default

Function to create an object of class WGCNANet
addGraphToCytoscape

Add network to Cytoscape
pickSIMoNeParam

Pick SIMoNe parameters
toCytoscape

Converts from igraph to Cytoscape object
ShortPathSTRINGNet.default

Function to create object of class ShortPathSTRINGNet
convertToDistGraph

Convert to distance graph from STRINGNet
getSIMoNeNet

Infer SIMoNe network from expression data
mapAttributes

Map attributes for toCytoscape()
compareGaussNetworks

Compare gaussian networks
export

Generic function to export network objects from package stringgaussnet.
plot.WGCNANet

Plot WGCNANet
print.WGCNANet

Print function for object of class WGCNANet.
addShortPathSTRINGNetMappings

Add Cytoscape mapping for ShortPathSTRINGNet
checkCytoscapeRunning

Check Cytoscape running
plot.SIMoNeNet

Plot SIMoNeNet
MultiNetworks

Generic function for objects of class MultiNetworks
applyStyle

Apply style to a network in Cytoscape
pickWGCNAParam

Pick WGCNA parameters
computeSimilarities

Compute similarities for WGCNA
resetCytoscapeSession

Reset Cytoscape session
print.FactorNetworks

Print function for object of class FactorNetworks
addSkeletonMappings

Add default mappings for Cytoscape styles
addWGCNANetMappings

Add Cytoscape mapping for WGCNANet
saveCytoscapeSession

Save Cytoscape session
getWGCNANet

Infer WGCNA network from expression data
print.SIMoNeNet

Print function for object of class SIMoNeNet.
getShortestPaths

Get shortest paths between given nodes in STRING network.
print.STRINGNet

Print function for object of class STRINGNet.
summary.SIMoNeNet

Summary function for object of class SIMoNeNet
summary.WGCNANet

Summary function for object of class WGCNANet
summary.STRINGNet

Summary function for object of class STRINGNet
selectInteractionTypes

Select interaction sources in STRINGNet object
computeCombinedScores

Compute STRING combined scores
findShortestPathways

Find shortest pathways between selected nodes
print.DEGeneExpr

Print function for object of class DEGeneExpr.
plot.FactorNetworks

Plot FactorNetworks
addSkeletonDefaults

Add default values for Cytoscape styles
WGCNANet

Generic function for objects of class WGCNANet
export.STRINGNet

Export STRINGNet
ShortPathSTRINGNet

Generic function for objects of class ShortPathSTRINGNet.
STRINGNet.default

Function to create an object of class STRINGNet
mergeGaussEdges

Merge gaussian networks edges
export.SIMoNeNet

Export SIMoNeNet
STRINGNet

Generic function for objects of class STRINGNet.
FilterEdges.ShortPathSTRINGNet

Filter edges in ShortPathSTRINGNet
getGenesInformations

Get gene annotations
mergeFactorEdges

Merge FactorNetworks edges
print.MultiNetworks

Print function for object of class MultiNetworks
MultiDEGeneExpr

Generic function for objects of class MultiDEGeneExpr
export.ShortPathSTRINGNet

Export ShortPathSTRINGNet
getMartDatasets

Gert maRt datasets
SpADataExpression

Data expression of the 75 DE genes identified by LIMMA in SpA sample data.
FactorNetworks

Generic function for objects of class FactorNetworks
MultiDEGeneExpr.default

Function to create an object of class MultiDEGeneExpr
SIMoNeNet

Generic function for objects of class SIMoNeNet
print.MultiDEGeneExpr

Print function for object of class MultiDEGeneExpr
applyLayout

Apply layout to a network in Cytoscape
addSTRINGNetMappings

Add Cytoscape mapping for STRINGNet
addMultiGraphToCytoscape

Add MultiNetworks to Cytoscape
compareFactorNetworks

Compare levels of FactorNetworks