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

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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.

Author
Ivana Ihnatova, Eva Budinska
Date of publication
None
Maintainer
Ivana Ihnatova <ihnatova@iba.muni.cz>
License
AGPL-3
Version
1.8.0

View on Bioconductor

Man pages

AdjacencyMatrix2Pathway
Function to coerce an adjacency matrix to a Pathway
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
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
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...

Files in this package

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