# PaxtoolsR: Pathway Analysis in R Using Pathway Commons

## TL;DR

PaxtoolsR is an R package that allows users to access and analyze pathway data from Pathway Commons, enabling pathway extraction, merging, and integration with local datasets.

## Contribution

PaxtoolsR introduces novel pathway datasets and advanced querying features for R users via the Pathway Commons webservice.

## Key findings

- The package supports extraction, merging, and validation of BioPAX pathway data.
- Users can integrate pathway data from Pathway Commons with local BioPAX datasets.
- The package is available on Bioconductor with documentation and tutorials for common tasks.

## Abstract

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. 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 this data with local BioPAX datasets.

The PaxtoolsR package is compatible with R 3.1.1 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 http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html. This plugin is free, open-source and licensed under the GNU Lesser General Public License (LGPL) v3.0.

paxtools@cbio.mskcc.org