Package index • ComplexMap

All functions

benchmarkParameters(): Benchmark Complex Refinement Parameters
buildComplexNetwork(): Build a Complex-Complex Interaction Network
computeMapTopology(): Compute Network Topology and Layout Coordinates
createComplexMap(): Create a Complete Complex Map Object
demoComplexes: Example Protein Complex List
evaluateComplexes(): Evaluate Predicted Protein Complexes Against a Reference Set
explore(): Explore a ComplexMap Object Interactively
exportNetwork(): Export a ComplexMap Network for External Tools
generateNodeAttributes(): Generate Node Attributes for a Complex Network
getEdgeTable(): Get the Edge Table from a ComplexMap Object
getExampleGmt(): Get the Path to an Example GMT File
getGmtFromFile(): Read a GMT File from a Local Path
getGoGmt(): Fetch Gene Ontology (GO) Gene Sets
getMsigdbGmt(): Fetch Gene Sets from MSigDB
getNodeTable(): Get the Node Table from a ComplexMap Object
getReactomeGmt(): Fetch Reactome Pathway Gene Sets
print(<ComplexMap>): Print Method for a ComplexMap Object
pruneNetwork(): Prune Network Edges Before Cytoscape Export
qcComplexList(): Perform Quality Control on a List of Protein Complexes
queryMap(): Query a ComplexMap Object
referenceComplexes: Reference Protein Complex Set (CORUM)
refineComplexList(): Refine a List of Protein Complexes by Size and Redundancy
runComplexEnrichment(): Run Gene Set Enrichment Analysis on a List of Complexes
runComplexMapApp(): Run the ComplexMap Interactive Explorer
scaleLayoutForCytoscape(): Scale Layout Coordinates for Cytoscape.js
toCytoscapeJSON(): Export a ComplexMap Object to Cytoscape.js JSON