Package: NCIgraph 1.60.0

Laurent Jacob

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.

Authors:Laurent Jacob

# Install 'NCIgraph' in R:

install.packages('NCIgraph', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

NCI.demo.cyList - 10 raw NCI networks from Nature curated pathways and BioCarta imported as graphNEL objects, for demonstration purpose

On BioConductor:NCIgraph-1.61.0(bioc 3.24)NCIgraph-1.60.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:9faaba6f41 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	154
linux-devel-x86_64	NOTE	216
source / vignettes	OK	179
linux-release-x86_64	NOTE	219
macos-release-arm64	NOTE	103
macos-oldrel-arm64	NOTE	86
windows-devel	NOTE	164
windows-release	NOTE	114
windows-oldrel	NOTE	124
wasm-release	OK	125

Last update: 2017-10-24
Started: 2013-11-01

Help page	Topics
Uses a breadth first search on a directed graph to identify which genes are regulated by a particular node in the graph	directedBFS
Identifies edges that should be merged to parse a NCI network	edgesToMerge
Loads networks from Cytoscape and parses them	getNCIPathways
Returns a list of @KEGGEdgeSubType objects describing each edge of the NCI network	getSubtype.NCIgraph
Assess whether a graph is a NCI graph	is.NCIgraph
Merges a given list of nodes in a graph	mergeNodes
10 raw NCI networks from Nature curated pathways and BioCarta imported as graphNEL objects, for demonstration purpose	NCI.demo.cyList
Class NCIgraph	NCIgraph-class
Takes a NCI network and transforms it into a simpler graph only representing inhibition/activation relationships between genes	parseNCInetwork
Transforms the network in a way that each Biochemical Reaction node pointing to a Complex points to what is regulated by the complex and updates the interaction types accordingly	propagateRegulation
Gives the entrezID corresponding to the nodes of a graph	translateNCI2GeneID