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.

AuthorAugustin Luna
Date of publicationNone
MaintainerAugustin Luna <lunaa@cbio.mskcc.org>
LicenseLGPL-3
Version1.8.0
https://github.com/BioPAX/paxtoolsr

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

Functions

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

Files

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

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