paxtoolsr: PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Version 1.10.0

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.

AuthorAugustin Luna
Bioconductor views GeneSetEnrichment GraphAndNetwork KEGG Network NetworkEnrichment Pathways Reactome Software SystemsBiology
Date of publicationNone
MaintainerAugustin Luna <lunaa@cbio.mskcc.org>
LicenseLGPL-3
Version1.10.0
URL https://github.com/BioPAX/paxtoolsr
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")

Getting started

Using PaxtoolsR: A BioPAX and Pathway Commons Tutorial in R

Popular man pages

addAttributeList: Add attributes using a list of vectors to an igraph object
convertSifnxIds: Convert IDs in a SIFNX
getPc: Get Pathway Commons BioPAX elements
getShortestPathSif: Get the shortest between two IDs (HGNC or CHEBI)
loadSifInIgraph: Load SIF as igraph Network
pcGraphQueries: Acceptable Pathway Commons Graph Queries
toSifnx: Converts BioPAX OWL file to extended binary SIF...
See all...

All man pages Function index File listing

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
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

Functions

addAttributeList Man page Source code
checkInputFile Source code
checkOutputFile Source code
convertSifToSpia Man page Source code
convertSifnxIds Man page Source code
convertToDF Man page Source code
convertToDT Man page Source code
downloadFile Man page Source code
downloadPc Man page
downloadPc2 Man page Source code
downloadSignedPC Man page Source code
extractIds Man page Source code
fetch Man page Source code
filterSif Man page Source code
getCacheFiles Man page Source code
getErrorMessage Man page Source code
getNeighbors Man page Source code
getPc Man page Source code
getPcRequest Source code
getPcUrl Man page Source code
getShortestPathSif Man page Source code
getSifInteractionCategories Man page Source code
graphPc Man page Source code
integrateBiopax Man page Source code
loadSifInIgraph Man page Source code
mapValues Man page Source code
mergeBiopax Man page Source code
onLoad Source code
pcDirections Man page Source code
pcFormats Man page Source code
pcGraphQueries Man page Source code
processPcRequest Man page Source code
readBiopax Man page Source code
readGmt Man page Source code
readSbgn Man page Source code
readSif Man page Source code
readSifnx Man page Source code
searchListOfVectors Man page Source code
searchPc Man page Source code
skip_on_bioc Man page Source code
splitSifnxByPathway Man page Source code
summarize Man page Source code
summarizeSif Man page Source code
toGSEA Man page Source code
toLevel3 Man page Source code
toSBGN Man page Source code
toSif Man page Source code
toSifnx Man page Source code
topPathways Man page Source code
traverse Man page Source code
validate Man page Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/addAttributeList.R
R/checkInputFile.R
R/checkOutputFile.R
R/convertSifToSpia.R
R/convertSifnxIds.R
R/convertToDF.R
R/convertToDT.R
R/convertToPathwayList.R
R/downloadFile.R
R/downloadPc.R
R/downloadPc2.R
R/downloadSignedPC.R
R/extractIds.R
R/fetch.R
R/filterSif.R
R/fromPsimi.R
R/getCacheFiles.R
R/getErrorMessage.R
R/getNeighbors.R
R/getPc.R
R/getPcRequest.R
R/getPcUrl.R
R/getShortestPathSif.R
R/getSifInteractionCategories.R
R/graphPc.R
R/integrateBiopax.R
R/loadSifInIgraph.R
R/mapValues.R
R/mergeBiopax.R
R/paxtoolsr.R
R/pcDirections.R
R/pcFormats.R
R/pcGraphQueries.R
R/processPcRequest.R
R/readBiopax.R
R/readGmt.R
R/readSbgn.R
R/readSif.R
R/readSifnx.R
R/searchListOfVectors.R
R/searchPc.R
R/splitSifnxByPathway.R
R/summarize.R
R/summarizeSif.R
R/toGSEA.R
R/toLevel3.R
R/toSBGN.R
R/toSif.R
R/toSifnx.R
R/topPathways.R
R/traverse.R
R/validate.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/using_paxtoolsr.R
inst/doc/using_paxtoolsr.Rmd
inst/doc/using_paxtoolsr.html
inst/extdata
inst/extdata/10523676-compact.xml
inst/extdata/REACT_12034-3.owl
inst/extdata/biopax3-short-metabolic-pathway.owl
inst/extdata/dna_replication.owl
inst/extdata/raf_map_kinase_cascade_reactome.owl
inst/extdata/tca_cycle.sif
inst/extdata/test_biopax.owl
inst/extdata/test_edgelist.txt
inst/extdata/test_gsea.gmt
inst/extdata/test_sbgn.xml
inst/extdata/test_sif.txt
inst/extdata/test_sifnx.txt
inst/extdata/test_sifnx2.txt
inst/extdata/test_sifnx_250.txt
inst/extdata/test_sifnx_sm.txt
inst/java
inst/java/paxtools-4.3.1.jar
inst/paxtoolsNotes.txt
java
java/README.md
man
man/addAttributeList.Rd
man/convertSifToSpia.Rd
man/convertSifnxIds.Rd
man/convertToDF.Rd
man/convertToDT.Rd
man/downloadFile.Rd
man/downloadPc2.Rd
man/downloadSignedPC.Rd
man/extractIds.Rd
man/fetch.Rd
man/filterSif.Rd
man/getCacheFiles.Rd
man/getErrorMessage.Rd
man/getNeighbors.Rd
man/getPc.Rd
man/getPcUrl.Rd
man/getShortestPathSif.Rd
man/getSifInteractionCategories.Rd
man/graphPc.Rd
man/integrateBiopax.Rd
man/loadSifInIgraph.Rd
man/mapValues.Rd
man/mergeBiopax.Rd
man/pcDirections.Rd
man/pcFormats.Rd
man/pcGraphQueries.Rd
man/processPcRequest.Rd
man/readBiopax.Rd
man/readGmt.Rd
man/readSbgn.Rd
man/readSif.Rd
man/readSifnx.Rd
man/searchListOfVectors.Rd
man/searchPc.Rd
man/skip_on_bioc.Rd
man/splitSifnxByPathway.Rd
man/summarize.Rd
man/summarizeSif.Rd
man/toGSEA.Rd
man/toLevel3.Rd
man/toSBGN.Rd
man/toSif.Rd
man/toSifnx.Rd
man/topPathways.Rd
man/traverse.Rd
man/validate.Rd
tests
tests/runTests.old
tests/testthat
tests/testthat.R
tests/testthat/test_pathwayCommons.R
tests/testthat/test_paxtools.R
vignettes
vignettes/using_paxtoolsr.Rmd
paxtoolsr documentation built on May 20, 2017, 9:46 p.m.