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

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
Date of publicationNone
MaintainerIvana Ihnatova <ihnatova@iba.muni.cz>
LicenseAGPL-3
Version1.8.0

View on Bioconductor

Functions

acc,Pathway,character-method Man page
addEdge,character,character,Pathway,numeric-method Man page
addNode,character,Pathway,list-method Man page
AdjacencyMatrix2pathway Man page
AdjacencyMatrix2Pathway Man page
changeDirection Man page
changeDirection,character,character,Pathway,character-method Man page
changeInteraction Man page
changeInteraction,character,character,Pathway,character,logical- Man page
clearNode,character,Pathway-method Man page
clipper Man page
collectWeightsPRS Man page
collectWeightsSPIA Man page
connComp,Pathway-method Man page
convertIdentifiersByVector Man page
convertIdentifiers,Pathway,character-method Man page
DEGraph Man page
degree,Pathway,character-method Man page
degree,Pathway,missing-method Man page
degtable Man page
edgemode,Pathway-method Man page
edgeNames,Pathway-method Man page
edges,Pathway,ANY-method Man page
edges,Pathway,character-method Man page
estimateCF Man page
graphNEL2pathway Man page
graphNEL2Pathway Man page
intersection,Pathway,Pathway-method Man page
isAdjacent,Pathway,character,character-method Man page
isConnected,Pathway-method Man page
isDirected,Pathway-method Man page
join,Pathway,Pathway-method Man page
KEGG2pathway Man page
KEGG2Pathway Man page
makeDefaultEdgeData Man page
mostEdges,Pathway-method Man page
nodes<-,Pathway,character-method Man page
nodes,Pathway-method Man page
numEdges,Pathway-method Man page
numNodes,Pathway-method Man page
numNoEdges,Pathway-method Man page
preparePathways Man page
prepareTIF Man page
PRS Man page
PWEA Man page
reduceGraph Man page
removeEdge,character,character,Pathway-method Man page
removeNode,character,Pathway-method Man page
res Man page
show,Pathway-method Man page
SPIA Man page
subGraph,character,Pathway-method Man page
TAPPA Man page
ToPASeq Man page
ToPASeq-deprecated Man page
ToPASeq-package Man page
TopologyGSA Man page
topo.sig Man page
union,Pathway,Pathway-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.