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bioRxiv · 10.1101/021105

PaxtoolsR: Pathway Analysis in R Using Pathway Commons

Augustin Luna·Özgün Babur·Bülent Arman Aksoy·Emek Demir·Chris Sander
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Abstract

PurposePaxtoolsR 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.\n\nAvailabilityThe 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.\n\nContactpaxtools@cbio.mskcc.org

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Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander. 2015-06-18. PaxtoolsR: Pathway Analysis in R Using Pathway Commons. https://doi.org/10.1101/021105

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