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

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

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

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