DOI: 10.18129/B9.bioc.paxtoolsr    

This is the development version of paxtoolsr; for the stable release version, see paxtoolsr.

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

Bioconductor version: Development (3.8)

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

Maintainer: Augustin Luna <lunaa at>

Citation (from within R, enter citation("paxtoolsr")):


To install this package, start R and enter:

if (!require("BiocManager"))
BiocManager::install("paxtoolsr", version = "devel")


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Using PaxtoolsR
PDF   Reference Manual
Text   NEWS


biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.15.0
In Bioconductor since BioC 3.0 (R-3.1) (4 years)
License LGPL-3
Depends R (>= 3.2), rJava (>= 0.9-8), XML
Imports httr, igraph, plyr, rjson, R.utils, data.table, jsonlite
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel,
SystemRequirements Java (>= 1.6)
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package paxtoolsr_1.15.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) paxtoolsr_1.15.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: