PT  - JOURNAL ARTICLE
AU  - Augustin Luna
AU  - Özgün Babur
AU  - Bülent Arman Aksoy
AU  - Emek Demir
AU  - Chris Sander
TI  - PaxtoolsR: Pathway Analysis in R Using Pathway Commons
AID  - 10.1101/021105
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 021105
4099  - http://biorxiv.org/content/early/2015/06/18/021105.short
4100  - http://biorxiv.org/content/early/2015/06/18/021105.full
AB  - 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. 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.Availability 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.Contact paxtools{at}cbio.mskcc.org