Learn R Programming
⚠️There's a newer version (1.1) of this package.Take me there.

stringgaussnet (version 1.0)

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

Description

A toolbox for a construction of PPI networks through STRING API 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.

Copy Link

Version

Install

install.packages('stringgaussnet')

Monthly Downloads

6

Version

1.0

License

GPL-3

Maintainer

Emmanuel Chaplais

Last Published

June 16th, 2015

Functions in stringgaussnet (1.0)

FilterEdges

Filter edges on network.
FilterEdges.SIMoNeNet

Filter edges in SIMoNeNet
convertAliases

Convert aliases
SIMoNeNet

Generic function for objects of class SIMoNeNet
convertToDistGraph

Convert to distance graph from STRINGNet
DEGeneExpr

Generic function for objects of class DEGeneExpr.
export.WGCNANet

Export WGCNANet
print.MultiDEGeneExpr

Print function for object of class MultiDEGeneExpr
FactorNetworks

Generic function for objects of class FactorNetworks
WGCNANet.default

Function to create an object of class WGCNANet
as.igraph.stringgaussnet

Convert stringgaussnet network into igraph
addSIMoNeNetMappings

Add Cytoscape mapping for SIMoNeNet
addSkeletonDefaults

Add default values for Cytoscape styles
addShortPathSTRINGNetMappings

Add Cytoscape mapping for ShortPathSTRINGNet
export.SIMoNeNet

Export SIMoNeNet
export.STRINGNet

Export STRINGNet
FilterEdges.FactorNetworks

Filter edges in FactorNetworks
MultiDEGeneExpr

Generic function for objects of class MultiDEGeneExpr
WGCNANet

Generic function for objects of class WGCNANet
compareFactorNetworks

Compare levels of FactorNetworks
applyLayout

Apply layout to a network in Cytoscape
pickSIMoNeParam

Pick SIMoNe parameters
plot.SIMoNeNet

Plot SIMoNeNet
compareGaussNetworks

Compare gaussian networks
addWGCNANetMappings

Add Cytoscape mapping for WGCNANet
getGenesInformations

Get gene annotations
addNetworkStyle

Add network style to Cytoscape
ShortPathSTRINGNet

Generic function for objects of class ShortPathSTRINGNet.
ShortPathSTRINGNet.default

Function to create object of class ShortPathSTRINGNet
addMultiGraphToCytoscape

Add MultiNetworks to Cytoscape
STRINGNet.default

Function to create an object of class STRINGNet
plot.WGCNANet

Plot WGCNANet
export.ShortPathSTRINGNet

Export ShortPathSTRINGNet
checkCytoscapeRunning

Check Cytoscape running
pickWGCNAParam

Pick WGCNA parameters
SpADEGenes

75 DE genes analysis results from LIMMA.
stringgaussnet-package

stringgaussnet
saveCytoscapeSession

Save Cytoscape session
resetCytoscapeSession

Reset Cytoscape session
addSTRINGNetMappings

Add Cytoscape mapping for STRINGNet
print.ShortPathSTRINGNet

Print function for object of class ShortPathSTRINGNet.
print.WGCNANet

Print function for object of class WGCNANet.
print.MultiNetworks

Print function for object of class MultiNetworks
computeCombinedScores

Compute STRING combined scores
summary.ShortPathSTRINGNet

Summary function for object of class ShortPathSTRINGNet
mergeGaussEdges

Merge gaussian networks edges
summary.WGCNANet

Summary function for object of class WGCNANet
getShortestPaths

Get shortest paths between given nodes in STRING network.
computeSimilarities

Compute similarities for WGCNA
SIMoNeNet.default

Function to create object of class SIMoneNet
summary.STRINGNet

Summary function for object of class STRINGNet
DEGeneExpr.default

Creation of DEGenesExpr object.
selectInteractionTypes

Select interaction sources in STRINGNet object
getSIMoNeNet

Infer SIMoNe network from expression data
FilterEdges.ShortPathSTRINGNet

Filter edges in ShortPathSTRINGNet
getMartDatasets

Gert maRt datasets
summary.SIMoNeNet

Summary function for object of class SIMoNeNet
FactorNetworks.default

Function to create an object of class FactorNetworks
print.DEGeneExpr

Print function for object of class DEGeneExpr.
mapAttributes

Map attributes for toCytoscape()
addSkeletonMappings

Add default mappings for Cytoscape styles
toCytoscape

Converts from igraph to Cytoscape object
export

Generic function to export network objects from package stringgaussnet.
MultiNetworks

Generic function for objects of class MultiNetworks
addGraphToCytoscape

Add network to Cytoscape
findShortestPathways

Find shortest pathways between selected nodes
getSTRINGNet

Get STRING network from gene identifiers
mergeFactorEdges

Merge FactorNetworks edges
print.STRINGNet

Print function for object of class STRINGNet.
print.SIMoNeNet

Print function for object of class SIMoNeNet.
STRINGNet

Generic function for objects of class STRINGNet.
SpADataExpression

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

Function to create an object of class MultiDEGeneExpr
addFactorGraphsToCytoscape

Add FactorNetworks object to Cytoscape
plot.FactorNetworks

Plot FactorNetworks
print.FactorNetworks

Print function for object of class FactorNetworks
applyStyle

Apply style to a network in Cytoscape
getWGCNANet

Infer WGCNA network from expression data
MultiNetworks.default

Function to create an object of class MultiNetworks
SpASamples

Samples description for SpA example data.