Package: paxtoolsr 1.39.0

Augustin Luna

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. Pathway Commons is a project by the Memorial Sloan-Kettering Cancer Center (MSKCC), Dana-Farber Cancer Institute (DFCI), and the University of Toronto. Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

Authors:Augustin Luna [aut, cre]

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paxtoolsr.pdf |paxtoolsr.html✨
paxtoolsr/json (API)
NEWS

# Install 'paxtoolsr' in R:
install.packages('paxtoolsr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/biopax/paxtoolsr/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:paxtoolsr-1.39.0(bioc 3.20)paxtoolsr-1.38.0(bioc 3.19)

genesetenrichmentgraphandnetworkpathwayssoftwaresystemsbiologynetworkenrichmentnetworkreactomekegg

46 exports 10 stars 5.92 score 44 dependencies 3 mentions 55 scripts 217 downloads

Last updated 5 months agofrom:444550a898. Checks:ERROR: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 30 2024
R-4.5-winERRORSep 30 2024
R-4.5-linuxERRORSep 30 2024
R-4.4-winERRORSep 30 2024
R-4.4-macERRORSep 30 2024
R-4.3-winERRORSep 30 2024
R-4.3-macERRORSep 30 2024

Exports:addAttributeListconvertDataFrameListsToVectorsconvertSifToGmtdownloadFiledownloadPc2downloadSignedPCfetchfilterSifgetCacheFilesgetErrorMessagegetNeighborsgetPcgetPcDatabaseNamesgetPcUrlgetShortestPathSifgetSifInteractionCategoriesgraphPcintegrateBiopaxloadSifInIgraphmapAttributesmapValuesmergeBiopaxpcDirectionspcFormatspcGraphQueriesprocessPcRequestreadBiopaxreadGmtreadPcPathwaysInforeadSbgnreadSifreadSifnxsearchListOfVectorssearchPcsplitSifnxByPathwaysummarizesummarizeSiftoCytoscapetoGSEAtoLevel3topPathwaystoSBGNtoSiftoSifnxtraversevalidate

Dependencies:askpassbitbit64clicliprcpp11crayoncurlfansigluehmshttrigraphjsonlitelatticelifecyclemagrittrMatrixmimeopensslpillarpkgconfigplyrprettyunitsprogressR.methodsS3R.ooR.utilsR6rappdirsRcppreadrrJavarjsonrlangsystibbletidyselecttzdbutf8vctrsvroomwithrXML

Readme and manuals

Help Manual

Help pageTopics
Add attributes using a list of vectors to an igraph objectaddAttributeList
Convert columns with list in data.frame to vectorconvertDataFrameListsToVectors
Convert SIF to GMTconvertSifToGmt
Check Cache and Download FiledownloadFile
Download Pathway Commons files (uses menu and cache)downloadPc downloadPc2
Download a SIF file containing only signed interactionsdownloadSignedPC
Fetch a set of IDs from a BioPAX OWL filefetch
Keep interactions in SIF network based on certain criteriafilterSif
List files in cache directorygetCacheFiles
Get Error Message for a Pathway Commons ErrorgetErrorMessage
Get the neighbors of a set of IDs in a BioPAX filegetNeighbors
Get Pathway Commons BioPAX elementsgetPc
Get a Pathway Commons DatabasesgetPcDatabaseNames
Get base Pathway Commons URLgetPcUrl
Get the shortest between two IDs (HGNC or CHEBI)getShortestPathSif
Get a list of categories of SIF interactionsgetSifInteractionCategories
Get Pathway Commons BioPAX elementsgraphPc
Integrate two BioPAX OWL files (DEPRECATED)integrateBiopax
Load SIF as igraph NetworkloadSifInIgraph
Map Attributes from igraph to Cytoscape JSONmapAttributes
Map values from One Vector to AnothermapValues
Merges two BioPAX OWL filesmergeBiopax
Acceptable Pathway Commons DirectionspcDirections
Acceptable Pathway Commons FormatspcFormats
Acceptable Pathway Commons Graph QueriespcGraphQueries
Process Pathway Commons request in various formatsprocessPcRequest
Read BioPAX files as XML documentsreadBiopax
Read in gene sets from GMT filesreadGmt
Read in Pathway Commons Pathways InformationreadPcPathwaysInfo
Read SBGN files as XML documentsreadSbgn
Read in a binary SIF filereadSif
Read in a Extended SIF filereadSifnx
Search List of VectorssearchListOfVectors
Search Pathway CommonssearchPc
Splits SIFNX entries into individual pathwayssplitSifnxByPathway
Summarize a BioPAX filesummarize
Summarize a SIF NetworksummarizeSif
Convert igraph to Cytoscape JSONtoCytoscape
Converts a BioPAX OWL file to a GSEA GMT gene settoGSEA
Convert a PSIMI or older BioPAX OWL file to BioPAX Level 3toLevel3
Retrieve top pathwaystopPathways
Convert a BioPAX OWL file to SBGNMLtoSBGN
Convert a BioPAX OWL file to SIFtoSif
Converts BioPAX OWL file to extended binary SIF representationtoSifnx
Access Pathway Commons using XPath-type expressionstraverse
Validate BioPAX filesvalidate