Package: NCIgraph 1.55.0

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.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-1.55.0(bioc 3.21)NCIgraph-1.54.0(bioc 3.20)

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

Last updated 2 months agofrom:bbee7a4e30. Checks:OK: 1 NOTE: 6. Indexed: yes.

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