NCIgraph: Pathways from the NCI Pathways Database
Version 1.24.0

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

AuthorLaurent Jacob
Bioconductor views GraphAndNetwork Pathways
Date of publicationNone
MaintainerLaurent Jacob <laurent.jacob@gmail.com>
LicenseGPL-3
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NCIgraph")

Popular 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
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...
See all...

All man pages Function index File listing

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

Functions

NCI.demo.cyList Man page
NCIgraph-class Man page
directedBFS Man page Source code
edgesToMerge Man page Source code
getNCIPathways Man page Source code
getSubtype.NCIgraph Man page Source code
is.NCIgraph Man page Source code
mergeNodes Man page Source code
parseNCInetwork Man page Source code
propagateRegulation Man page Source code
translateNCI2GeneID Man page Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/allClasses.R
R/directedBFS.R
R/edgesToMerge.R
R/getNCIPathways.R
R/getSubtype.NCIgraph.R
R/is.NCIgraph.R
R/mergeNodes.R
R/parseNCInetwork.R
R/propagateRegulation.R
R/translateNCI2GeneID.R
build
build/vignette.rds
data
data/NCIgraphVignette.RData
inst
inst/COPYING
inst/doc
inst/doc/NCIgraph.R
inst/doc/NCIgraph.Rnw
inst/doc/NCIgraph.pdf
inst/extdata
inst/extdata/getNCIPathways.Rex
inst/extdata/getSubtype.NCIgraph.Rex
inst/extdata/parseNCInetwork.Rex
inst/extdata/translateNCI2GeneID.Rex
inst/scripts
inst/scripts/generateManPages.R
man
man/NCI.demo.cyList.Rd
man/NCIgraph.Rd
man/directedBFS.Rd
man/edgesToMerge.Rd
man/getNCIPathways.Rd
man/getSubtype.NCIgraph.Rd
man/is.NCIgraph.Rd
man/mergeNodes.Rd
man/parseNCInetwork.Rd
man/propagateRegulation.Rd
man/translateNCI2GeneID.Rd
vignettes
vignettes/NCIgraph-bibli.bib
vignettes/NCIgraph.Rnw
NCIgraph documentation built on May 20, 2017, 9:16 p.m.

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

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

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