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

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

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