# GRAPH Interaction from pathway Topological Environment

## Documentation for package ‘graphite’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

biocarta | BioCarta pathways
convertIdentifiers | Convert the node identifiers of a pathway.
cytoscapePlot | Plot a pathway graph in Cytoscape
edges-method | Class '"pathway"'
humancyc | Humancyc pathways
kegg | KEGG pathways
nci | NCI pathways
nodes-method | Class '"pathway"'
panther | Panther pathways
pathway-class | Class '"pathway"'
pathwayGraph | Graph representing the topology of a pathway
prepareSPIA | Prepare pathway dataset needed by runSPIA.
reactome | Reactome pathways
runClipper | Run a topological analysis on an expression dataset using the clipper.
runClipperMulti | Run topological analyses on an expression dataset, calling clipper over all the pathways in a list.
runDEGraph | Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti | Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.
runSPIA | Run SPIA analysis
runTopologyGSA | Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSAMulti | Run topological analyses on an expression dataset, calling topologyGSA over all the pathways in a list.
show-method | Class '"pathway"'
spike | SPIKE pathways