R: Pathways from the NCI Pathways Database

# Pathways from the NCI Pathways Database

## Documentation for package ‘NCIgraph’ version 1.60.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

directedBFS | Uses a breadth first search on a directed graph to identify which genes are regulated by a particular node in the graph
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 edge of the NCI network
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 imported as graphNEL objects, for demonstration purpose
NCIgraph-class | Class NCIgraph
parseNCInetwork | Takes a NCI network and transforms it into a simpler graph only representing inhibition/activation relationships between genes
propagateRegulation | 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
translateNCI2GeneID | Gives the entrezID corresponding to the nodes of a graph