title: PaxtoolsR: pathway analysis in R using Pathway Commons.
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 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.
  
  
  
  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 http://www.bioconductor.org/packages/paxtoolsr This plugin is free, open-source and licensed under the LGPL-3.
  
  
  
  paxtools@cbio.mskcc.org or lunaa@cbio.mskcc.org.
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Augustin
authors.initials: A
authors.lastname: Luna
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Özgün
authors.initials: Ö
authors.lastname: Babur
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Bülent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
authors.affiliation: Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004282:Documentation; D011381:Programming Languages; D012984:Software