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 |