@article {Luna021105, author = {Augustin Luna and {\"O}zg{\"u}n Babur and B{\"u}lent Arman Aksoy and Emek Demir and Chris Sander}, title = {PaxtoolsR: Pathway Analysis in R Using Pathway Commons}, elocation-id = {021105}, year = {2015}, doi = {10.1101/021105}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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}, URL = {https://www.biorxiv.org/content/early/2015/06/18/021105}, eprint = {https://www.biorxiv.org/content/early/2015/06/18/021105.full.pdf}, journal = {bioRxiv} }