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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ToPASeq")
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
Version1.8.0

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

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.