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Enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons web service for users of the R language. Features include the extraction, merging, and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons web service allowing users to query, extract, and retrieve data and integrate this data with local BioPAX datasets.

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PaxtoolsR classification

PaxtoolsR specifications

Software type:
Restrictions to use:
Programming languages:
Java, R
Computer skills:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
GNU Lesser General Public License version 3.0
rJava, XML, RCurl, rjson, plyr

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PaxtoolsR support



  • Augustin Luna <>


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Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Funding source(s)

This research was supported by the US National Institutes of Health grant U41 HG006623-02 and through funding for the National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS) under grant P41 GM103504.

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.