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

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Bioconductor version: Development (3.19)

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.

Author: Augustin Luna [aut, cre]

Maintainer: Augustin Luna <lunaa at cbio.mskcc.org>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

Using PaxtoolsR HTML R Script
Reference Manual PDF


biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License LGPL-3
Depends R (>= 3.2), rJava (>= 0.9-8), methods, XML
Imports utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr, rappdirs
System Requirements Java (>= 1.6)
URL https://github.com/BioPAX/paxtoolsr
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Suggests testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
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Follow Installation instructions to use this package in your R session.

Source Package paxtoolsr_1.37.0.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/paxtoolsr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/paxtoolsr
Bioc Package Browser https://code.bioconductor.org/browse/paxtoolsr/
Package Short Url https://bioconductor.org/packages/paxtoolsr/
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