PaxtoolsR: pathway analysis in R using Pathway Commons

Bioinformatics. 2016 Apr 15;32(8):1262-4. doi: 10.1093/bioinformatics/btv733. Epub 2015 Dec 18.


Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. 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 webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets.

Availability and implementation: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at This plugin is free, open-source and licensed under the LGPL-3.

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MeSH terms

  • Computational Biology / methods*
  • Documentation
  • Programming Languages
  • Software*