ToPASeq: Package for Topology-based Pathway Analysis of RNASeq data
Version 1.10.0

Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a single pathway.

AuthorIvana Ihnatova, Eva Budinska
Bioconductor views DifferentialExpression GeneExpression GraphAndNetwork Microarray NetworkEnrichment Pathways RNASeq Software Visualization
Date of publicationNone
MaintainerIvana Ihnatova <ihnatova@iba.muni.cz>
LicenseAGPL-3
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ToPASeq")

Getting started

Package overview

Popular man pages

convertIdentifiersByVector: Function to convert identifiers in pathways by user specified...
Deprecated: Deprecated functions in package 'ToPASeq'
KEGG2pathway: Function to parse KEGG KGML file into a Pathway
preparePathways: Function to prepare pathways for topology-based pathway...
PRS: Function to use PRS method on microarray or RNA-Seq data
reduceRraph: Function to reduce the pathway graph
SPIA: Function to use SPIA method on microarray or RNA-Seq data
See all...

All man pages Function index File listing

Man pages

AdjacencyMatrix2Pathway: Function to coerce an adjacency matrix to a Pathway
CePa: Function to use CePa method on microarray or RNA-Seq data
Clipper: Function to use clipper method on microarray or RNA-Seq data
collectWeightsPRS: Function to calculate gene-level weights for topology-based...
convertIdentifiersByVector: Function to convert identifiers in pathways by user specified...
defaultEdgeAttrs: Creates auxiliary data needed for SPIA method
DEGraph: Function to use DEGraph method on microarray or RNA-Seq data
Deprecated: Deprecated functions in package 'ToPASeq'
estimateCF: Function to estimate multi-subunit protein complexes and gene...
graphNEL2Pathway: Function to coerce a graphNEL to a Pathway
KEGG2pathway: Function to parse KEGG KGML file into a Pathway
parseKEGG: Function to covert KEGG pathways for topology-based pathway...
pathway-class: Class '"Pathway"'
preparePathways: Function to prepare pathways for topology-based pathway...
PRS: Function to use PRS method on microarray or RNA-Seq data
PWEA: Function to use PWEA method on microarray or RNA-Seq data
reduceRraph: Function to reduce the pathway graph
res: Function to extract parts of object
SPIA: Function to use SPIA method on microarray or RNA-Seq data
SPIA4analysis: Function to further process pathways for SPIA
TAPPA: Function to use TAPPA method on microarray or RNA-Seq data
ToPASeq-package: Package for topology-based pathway analysis of microarray and...
TopologyGSA: Function to use TopologyGSA method on microarray or RNA-Seq...

Functions

AdjacencyMatrix2Pathway Man page Source code
AdjacencyMatrix2pathway Man page Source code
BigPaths Source code
CLIPPER Source code
CLIPPERfast Source code
CMT Source code
CVT Source code
CePa Man page Source code
CePaORA Source code
CePaSingle Source code
CePaWeights Source code
CePanoDEG Source code
CheckNames Source code
CommonGenes Source code
DAGOnly Source code
DEGraph Man page Source code
DEGraphnoDEG Source code
FewEdges Source code
KEGG2Pathway Man page Source code
KEGG2pathway Man page Source code
MoralizeMG Source code
PMT Source code
PRS Man page Source code
PRSSingle Source code
PRSnoDEG Source code
PRSweights Source code
PVT Source code
PWEA Man page Source code Source code
PWEASingle Source code
PWEAscore Source code
SPIA Man page Source code
SPIA2graph Man page Source code
SPIA4analysis Man page Source code
SPIA4plot Source code
SPIASingle Source code
SPIAnoDEG Source code
SPIAweights Source code
TAPPA Man page Source code
TAPPASingle Source code
TAPPAnoDEG Source code
TIF Source code
ToPASeq Man page
ToPASeq-deprecated Man page
ToPASeq-package Man page
TopologyGSA Man page Source code
TopologyGSAnoDEG Source code
acc,Pathway,character-method Man page
accCpp Source code
addEdge,character,character,Pathway,numeric-method Man page
addNode,character,Pathway,list-method Man page
adjustAttr Source code
adjustAttrCli Source code
applyReduction Source code
applyTh Source code
between Source code
betweenness Source code
buildGraphNEL Source code
calculatePCI Source code
canonicalEdgeNames Source code
catchErr Source code
changeDirection Man page
changeDirection,character,character,Pathway,character-method Man page
changeInteraction Man page
changeInteraction,character,character,Pathway,character,logical- Man page
checkDEandAll Source code
checkNodes Source code
checkPkgVersion Source code
clearNode,character,Pathway-method Man page
cli Source code
clipper Man page Source code
clipperSingle Source code
clippernoDEG Source code
clique.edges Source code
colMax Source code
colMin Source code
collectWeightsPRS Man page Source code
collectWeightsSPIA Man page Source code
combfunc Source code
connComp,Pathway-method Man page
convertIdentifiers,Pathway,character-method Man page
convertIdentifiersByVector Man page Source code
degraph Source code
degree,Pathway,character-method Man page
degree,Pathway,missing-method Man page
degtable Man page Source code
degtable.topResult Source code
downstreamCpp Source code
drawGraph Source code
drawHead Source code
drawNodesPies2 Source code
drawSPIA Source code
edLi Source code
edgeNames,Pathway-method Man page
edgemode,Pathway-method Man page
edges,Pathway,ANY-method Man page
edges,Pathway,character-method Man page
edgetypeslegend Source code
eliminateNode Source code
estimateCF Man page Source code
estimateCov Source code
estimateCovPool Source code
extractsubset Source code
filterByTag Source code Source code
filterSPIA Source code
getNodeCex Source code
getRenderPar Source code
getdatp Source code
graphNEL2Pathway Man page Source code
graphNEL2pathway Man page Source code
gseaScores Source code
gseaScoresCols Source code
headline Source code
hote Source code
hotePaired Source code
indegree Source code
inreach Source code
intersection,Pathway,Pathway-method Man page
isAdjacent,Pathway,character,character-method Man page
isComplex Source code
isConnected,Pathway-method Man page
isDirected,Pathway-method Man page
join,Pathway,Pathway-method Man page
makeBreaks Source code
makeDefaultEdgeData Man page Source code
makeEdgeList Source code
makeLegend Source code
makeNodeSizeLegend Source code
makeNodeTable Source code
mergeDesc Source code
mergeEdges Source code
mostEdges,Pathway-method Man page
mult.test Source code
nodes,Pathway-method Man page
nodes<-,Pathway,character-method Man page
normalizationTAPPA Source code
notPTIF Source code
numEdges,Pathway-method Man page
numNoEdges,Pathway-method Man page
numNodes,Pathway-method Man page
outdegree Source code
outreach Source code
parDE Source code
parseAsCePa Source code
parseAsDEGraph Source code
parseAsPRS Source code
parseAsPWEA Source code
parseAsSPIA Source code
parseKEGG Man page Source code
parsePerms Source code
pieRad Source code
plot.topResult Source code
plotCliques Source code
plotRagraph Source code
prepareData Source code
prepareEdges Source code
preparePathways Man page Source code
preparePerms Source code
preparePermsCePap Source code
preparePermsPWEA Source code
prepareSPIA2 Source code
prepareTIF Man page Source code
print.topResult Source code
procParams Source code
processDEGraph Source code
processMA Source code
processRNAseq Source code
prs Source code
pwea Source code
reactionsCePa Source code
reactionsPRS Source code
reactionsPWEA Source code
reduceGraph Man page Source code
removeEdge,character,character,Pathway-method Man page
removeNode,character,Pathway-method Man page
renderEdgesTypes2 Source code
renderOrig Source code
renderReduced Source code
renderSpline Source code
res Man page Source code
res.topResult Source code
rotate Source code
runCliqueVarTest Source code
runPathwayVarTest Source code
show,Pathway-method Man page
spia Source code
subGraph,character,Pathway-method Man page
summary.topResult Source code
symmetricEdges Source code
tappa Source code
testCliques Source code
testDESeq2 Source code
testDESeq2perm Source code
testMA Source code
testRNAseq Source code
testedgeR Source code
testvoomlimma Source code
testvstlimma Source code
text.lines Source code
topo.sig Man page Source code
topo.sig.topResult Source code
topologyGSA Source code
transformPathway Source code
union,Pathway,Pathway-method Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/AdjacencyMatrix2pathway.R
R/KEGG2pathway.r
R/RcppExports.R
R/convertIdentifiersByVector.R
R/drawingFunctions.r
R/estimateCF.r
R/graf.r
R/grafikastypmihran.R
R/graphNEL2pathway.R
R/isComplex.R
R/makeDefaultEdgeData.r
R/parsingByMethod.r
R/pathway_methods.R
R/pomocne.R
R/prepareData.r
R/prepisCePa.R
R/prepisClipper.r
R/prepisDEGraph.r
R/prepisPRS.r
R/prepisPWEA.r
R/prepisSPIA.r
R/prepisTAPPA.R
R/prepisTopologyGSA.r
R/reduceGraph.R
R/testsDEG.R
R/wrappers.r
R/wrappersnoDEG.r
Rplots.pdf
build
build/vignette.rds
inst
inst/doc
inst/doc/ToPASeq.R
inst/doc/ToPASeq.Rnw
inst/doc/ToPASeq.pdf
inst/extdata
inst/extdata/hsa04610.xml
inst/unitTests
inst/unitTests/test_AdjacencyMatrix2pathway.R
inst/unitTests/test_convertIdentifiersByVector.R
inst/unitTests/test_graphNEL2pathway.R
inst/unitTests/test_makeDefaultEdgeData.R
inst/unitTests/test_topoAnalysis.r
man
man/AdjacencyMatrix2Pathway.Rd
man/CePa.Rd
man/Clipper.Rd
man/DEGraph.Rd
man/Deprecated.Rd
man/KEGG2pathway.Rd
man/PRS.Rd
man/PWEA.Rd
man/SPIA.Rd
man/SPIA4analysis.Rd
man/TAPPA.Rd
man/ToPASeq-package.Rd
man/TopologyGSA.Rd
man/collectWeightsPRS.Rd
man/convertIdentifiersByVector.Rd
man/defaultEdgeAttrs.Rd
man/estimateCF.Rd
man/graphNEL2Pathway.Rd
man/parseKEGG.Rd
man/pathway-class.Rd
man/preparePathways.Rd
man/reduceRraph.Rd
man/res.Rd
src
src/RcppExports.cpp
src/accCpp.cpp
src/betweeness.cpp
src/colMinMax.cpp
src/downstream.cpp
tests
tests/runTests.R
vignettes
vignettes/ToPASeq.Rnw
vignettes/plot.pdf
ToPASeq documentation built on May 20, 2017, 10:50 p.m.

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