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

The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

Author
Augustin Luna
Date of publication
None
Maintainer
Augustin Luna <lunaa@cbio.mskcc.org>
License
LGPL-3
Version
1.8.0
URLs

View on Bioconductor

Man pages

addAttributeList
Add attributes using a list of vectors to an igraph object
convertSifnxIds
Convert IDs in a SIFNX
convertSifToSpia
Convert SIF Interaction Types to SPIA types
convertToDF
Convert Results from readSifnx to data.frame
convertToDT
Convert Results from readSifnx to data.table
downloadFile
Check Cache and Download File
downloadPc2
Download Pathway Commons files (uses menu and cache)
downloadSignedPC
Download a SIF file containing only signed interactions
extractIds
Extract IDs from an Extended SIF
fetch
Fetch a set of IDs from a BioPAX OWL file
filterSif
Keep interactions in SIF network based on certain criteria
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
getShortestPathSif
Get the shortest between two IDs (HGNC or CHEBI)
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...
traverse
Access Pathway Commons using XPath-type expressions
validate
Validate BioPAX files

Files in this package

paxtoolsr/.Rinstignore
paxtoolsr/DESCRIPTION
paxtoolsr/NAMESPACE
paxtoolsr/NEWS
paxtoolsr/R
paxtoolsr/R/addAttributeList.R
paxtoolsr/R/checkInputFile.R
paxtoolsr/R/checkOutputFile.R
paxtoolsr/R/convertSifToSpia.R
paxtoolsr/R/convertSifnxIds.R
paxtoolsr/R/convertToDF.R
paxtoolsr/R/convertToDT.R
paxtoolsr/R/convertToPathwayList.R
paxtoolsr/R/downloadFile.R
paxtoolsr/R/downloadPc.R
paxtoolsr/R/downloadPc2.R
paxtoolsr/R/downloadSignedPC.R
paxtoolsr/R/extractIds.R
paxtoolsr/R/fetch.R
paxtoolsr/R/filterSif.R
paxtoolsr/R/fromPsimi.R
paxtoolsr/R/getCacheFiles.R
paxtoolsr/R/getErrorMessage.R
paxtoolsr/R/getNeighbors.R
paxtoolsr/R/getPc.R
paxtoolsr/R/getPcRequest.R
paxtoolsr/R/getPcUrl.R
paxtoolsr/R/getShortestPathSif.R
paxtoolsr/R/getSifInteractionCategories.R
paxtoolsr/R/graphPc.R
paxtoolsr/R/idMapping.R
paxtoolsr/R/integrateBiopax.R
paxtoolsr/R/loadSifInIgraph.R
paxtoolsr/R/mapValues.R
paxtoolsr/R/mergeBiopax.R
paxtoolsr/R/paxtoolsr.R
paxtoolsr/R/pcDirections.R
paxtoolsr/R/pcFormats.R
paxtoolsr/R/pcGraphQueries.R
paxtoolsr/R/processPcRequest.R
paxtoolsr/R/readBiopax.R
paxtoolsr/R/readGmt.R
paxtoolsr/R/readSbgn.R
paxtoolsr/R/readSif.R
paxtoolsr/R/readSifnx.R
paxtoolsr/R/searchListOfVectors.R
paxtoolsr/R/searchPc.R
paxtoolsr/R/splitSifnxByPathway.R
paxtoolsr/R/summarize.R
paxtoolsr/R/summarizeSif.R
paxtoolsr/R/toGSEA.R
paxtoolsr/R/toLevel3.R
paxtoolsr/R/toSBGN.R
paxtoolsr/R/toSif.R
paxtoolsr/R/toSifnx.R
paxtoolsr/R/topPathways.R
paxtoolsr/R/traverse.R
paxtoolsr/R/validate.R
paxtoolsr/build
paxtoolsr/build/vignette.rds
paxtoolsr/inst
paxtoolsr/inst/CITATION
paxtoolsr/inst/doc
paxtoolsr/inst/doc/using_paxtoolsr.R
paxtoolsr/inst/doc/using_paxtoolsr.Rmd
paxtoolsr/inst/doc/using_paxtoolsr.html
paxtoolsr/inst/extdata
paxtoolsr/inst/extdata/10523676-compact.xml
paxtoolsr/inst/extdata/REACT_12034-3.owl
paxtoolsr/inst/extdata/biopax3-short-metabolic-pathway.owl
paxtoolsr/inst/extdata/dna_replication.owl
paxtoolsr/inst/extdata/raf_map_kinase_cascade_reactome.owl
paxtoolsr/inst/extdata/tca_cycle.sif
paxtoolsr/inst/extdata/test_biopax.owl
paxtoolsr/inst/extdata/test_edgelist.txt
paxtoolsr/inst/extdata/test_gsea.gmt
paxtoolsr/inst/extdata/test_sbgn.xml
paxtoolsr/inst/extdata/test_sif.txt
paxtoolsr/inst/extdata/test_sifnx.txt
paxtoolsr/inst/extdata/test_sifnx2.txt
paxtoolsr/inst/extdata/test_sifnx_250.txt
paxtoolsr/inst/extdata/test_sifnx_sm.txt
paxtoolsr/inst/java
paxtoolsr/inst/java/paxtools-4.3.1.jar
paxtoolsr/inst/paxtoolsNotes.txt
paxtoolsr/java
paxtoolsr/java/README.md
paxtoolsr/man
paxtoolsr/man/addAttributeList.Rd
paxtoolsr/man/convertSifToSpia.Rd
paxtoolsr/man/convertSifnxIds.Rd
paxtoolsr/man/convertToDF.Rd
paxtoolsr/man/convertToDT.Rd
paxtoolsr/man/downloadFile.Rd
paxtoolsr/man/downloadPc2.Rd
paxtoolsr/man/downloadSignedPC.Rd
paxtoolsr/man/extractIds.Rd
paxtoolsr/man/fetch.Rd
paxtoolsr/man/filterSif.Rd
paxtoolsr/man/getCacheFiles.Rd
paxtoolsr/man/getErrorMessage.Rd
paxtoolsr/man/getNeighbors.Rd
paxtoolsr/man/getPc.Rd
paxtoolsr/man/getPcUrl.Rd
paxtoolsr/man/getShortestPathSif.Rd
paxtoolsr/man/getSifInteractionCategories.Rd
paxtoolsr/man/graphPc.Rd
paxtoolsr/man/idMapping.Rd
paxtoolsr/man/integrateBiopax.Rd
paxtoolsr/man/loadSifInIgraph.Rd
paxtoolsr/man/mapValues.Rd
paxtoolsr/man/mergeBiopax.Rd
paxtoolsr/man/pcDirections.Rd
paxtoolsr/man/pcFormats.Rd
paxtoolsr/man/pcGraphQueries.Rd
paxtoolsr/man/processPcRequest.Rd
paxtoolsr/man/readBiopax.Rd
paxtoolsr/man/readGmt.Rd
paxtoolsr/man/readSbgn.Rd
paxtoolsr/man/readSif.Rd
paxtoolsr/man/readSifnx.Rd
paxtoolsr/man/searchListOfVectors.Rd
paxtoolsr/man/searchPc.Rd
paxtoolsr/man/skip_on_bioc.Rd
paxtoolsr/man/splitSifnxByPathway.Rd
paxtoolsr/man/summarize.Rd
paxtoolsr/man/summarizeSif.Rd
paxtoolsr/man/toGSEA.Rd
paxtoolsr/man/toLevel3.Rd
paxtoolsr/man/toSBGN.Rd
paxtoolsr/man/toSif.Rd
paxtoolsr/man/toSifnx.Rd
paxtoolsr/man/topPathways.Rd
paxtoolsr/man/traverse.Rd
paxtoolsr/man/validate.Rd
paxtoolsr/tests
paxtoolsr/tests/runTests.old
paxtoolsr/tests/testthat
paxtoolsr/tests/testthat.R
paxtoolsr/tests/testthat/test_pathwayCommons.R
paxtoolsr/tests/testthat/test_paxtools.R
paxtoolsr/vignettes
paxtoolsr/vignettes/using_paxtoolsr.Rmd