PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons


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Documentation for package ‘paxtoolsr’ version 1.2.11

Help Pages

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
topPathways Retrieve top pathways
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
traverse Access Pathway Commons using XPath-type expressions
validate Validate BioPAX files