convertSifnxIds | Convert IDs in a SIFNX |
convertSifToSpia | Convert SIF Interaction Types to SPIA types |
convertToDT | Convert Results from readSifnx to data.table |
downloadFile | Check Cache and Download File |
downloadPc | Download Pathway Commons data (DEPRECATED) |
downloadPc2 | Download Pathway Commons files (uses menu and cache) |
extractIds | Extract IDs from an Extended SIF |
fetch | Fetch a set of IDs from a BioPAX OWL file |
filterSif | Keep interactions in SIF network of certain interaction types |
getCacheFiles | List files in cache directory |
getErrorMessage | Get Error Message for a Pathway Commons Error |
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 |
getSifInteractionCategories | Get a list of categories of SIF interactions |
graphPc | Get Pathway Commons BioPAX elements |
idMapping | Map IDs to Primary Uniprot or ChEBI IDs |
integrateBiopax | Integrate two BioPAX OWL files (DEPRECATED) |
loadSifInIgraph | Load SIF as igraph Network |
mapValues | Map values from One Vector to Another |
mergeBiopax | Merges two BioPAX OWL files |
pcDirections | Acceptable Pathway Commons Directions |
pcFormats | Acceptable Pathway Commons Formats |
pcGraphQueries | Acceptable Pathway Commons Graph Queries |
processPcRequest | Process Pathway Commons request in various formats |
readBiopax | Read BioPAX files as XML documents |
readGmt | Read in gene sets from GMT files |
readSbgn | Read SBGN files as XML documents |
readSif | Read in a binary SIF file |
readSifnx | Read in a Extended SIF file |
searchListOfVectors | Search List of Vectors |
searchPc | Search Pathway Commons |
skip_on_bioc | Skip a test if on Bioconductor |
splitSifnxByPathway | Splits SIFNX entries into individual pathways |
summarize | Summarize a BioPAX file |
summarizeSif | Summarize a SIF Network |
toGSEA | Converts a BioPAX OWL file to a GSEA GMT gene set |
toLevel3 | Convert a PSIMI or older 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 |