downloadPc              Download Pathway Commons data
fetch                   Fetch a set of IDs from a BioPAX OWL file
fromPsimi               Read PSIMI file
getNeighbors            Get the neighbors of a set of IDs in a BioPAX
                        file
getPc                   Get Pathway Commons BioPAX elements
getPcUrl                Get base Pathway Commons URL
graphPc                 Get Pathway Commons BioPAX elements
idMapping               Map IDs to Primary Uniprot or ChEBI IDs
integrateBiopax         Integrate two BioPAX OWL files (DEPRECATED)
mergeBiopax             Merges two BioPAX OWL files
pcDirections            Acceptable Pathway Commons Directions
pcFormats               Acceptable Pathway Commons Formats
pcGraphQueries          Acceptable Pathway Commons Graph Queries
readGmt                 Read in gene sets from GMT files
searchPc                Search Pathway Commons
splitSifnx              Split Extended SIF File
summarize               Summarize a BioPAX file
toGSEA                  Converts a BioPAX OWL file to a GSEA GMT gene
                        set
toLevel3                Convert a BioPAX OWL file to BioPAX Level 3
toSBGN                  Convert a BioPAX OWL file to SBGNML
toSif                   Convert a BioPAX OWL file to SIF
toSifnx                 Converts BioPAX OWL file to extended binary SIF
                        representation
topPathways             Retrieve top pathways
traverse                Access Pathway Commons using XPath-type
                        expressions
validate                Validate BioPAX files
