NCIgraph: Pathways from the NCI Pathways Database

Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.

Author
Laurent Jacob
Date of publication
None
Maintainer
Laurent Jacob <laurent.jacob@gmail.com>
License
GPL-3
Version
1.22.0

View on Bioconductor

Man pages

directedBFS
Uses a breadth first search on a directed graph to identify...
edgesToMerge
Identifies edges that should be merged to parse a NCI network
getNCIPathways
Loads networks from Cytoscape and parses them
getSubtype.NCIgraph
Returns a list of @KEGGEdgeSubType objects describing each...
is.NCIgraph
Assess whether a graph is a NCI graph
mergeNodes
Merges a given list of nodes in a graph
NCI.demo.cyList
10 raw NCI networks from Nature curated pathways and BioCarta...
NCIgraph
Class NCIgraph
parseNCInetwork
Takes a NCI network and transforms it into a simpler graph...
propagateRegulation
Transforms the network in a way that each Biochemical...
translateNCI2GeneID
Gives the entrezID corresponding to the nodes of a graph

Files in this package

NCIgraph/.BBSoptions
NCIgraph/DESCRIPTION
NCIgraph/NAMESPACE
NCIgraph/R
NCIgraph/R/allClasses.R
NCIgraph/R/directedBFS.R
NCIgraph/R/edgesToMerge.R
NCIgraph/R/getNCIPathways.R
NCIgraph/R/getSubtype.NCIgraph.R
NCIgraph/R/is.NCIgraph.R
NCIgraph/R/mergeNodes.R
NCIgraph/R/parseNCInetwork.R
NCIgraph/R/propagateRegulation.R
NCIgraph/R/translateNCI2GeneID.R
NCIgraph/build
NCIgraph/build/vignette.rds
NCIgraph/data
NCIgraph/data/NCIgraphVignette.RData
NCIgraph/inst
NCIgraph/inst/COPYING
NCIgraph/inst/doc
NCIgraph/inst/doc/NCIgraph.R
NCIgraph/inst/doc/NCIgraph.Rnw
NCIgraph/inst/doc/NCIgraph.pdf
NCIgraph/inst/extdata
NCIgraph/inst/extdata/getNCIPathways.Rex
NCIgraph/inst/extdata/getSubtype.NCIgraph.Rex
NCIgraph/inst/extdata/parseNCInetwork.Rex
NCIgraph/inst/extdata/translateNCI2GeneID.Rex
NCIgraph/inst/scripts
NCIgraph/inst/scripts/generateManPages.R
NCIgraph/man
NCIgraph/man/NCI.demo.cyList.Rd
NCIgraph/man/NCIgraph.Rd
NCIgraph/man/directedBFS.Rd
NCIgraph/man/edgesToMerge.Rd
NCIgraph/man/getNCIPathways.Rd
NCIgraph/man/getSubtype.NCIgraph.Rd
NCIgraph/man/is.NCIgraph.Rd
NCIgraph/man/mergeNodes.Rd
NCIgraph/man/parseNCInetwork.Rd
NCIgraph/man/propagateRegulation.Rd
NCIgraph/man/translateNCI2GeneID.Rd
NCIgraph/vignettes
NCIgraph/vignettes/NCIgraph-bibli.bib
NCIgraph/vignettes/NCIgraph.Rnw