title: PharmacoGx: an R package for analysis of large pharmacogenomic datasets.
abstract: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data.
  
  
  
  PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub.
  
  
  
  bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
authors.forename: Petr
authors.initials: P
authors.lastname: Smirnov
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Zhaleh
authors.initials: Z
authors.lastname: Safikhani
authors.affiliation: Institut De Recherches Cliniques De Montréal, Montreal, QC, Canada.
authors.forename: Nehme
authors.initials: N
authors.lastname: El-Hachem
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
authors.forename: Adrian
authors.initials: A
authors.lastname: She
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels, Belgium, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Catharina
authors.initials: C
authors.lastname: Olsen
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Freeman
authors.affiliation: Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA, Department of Bioinformatics, Boston University, Boston, MA, USA.
authors.forename: Heather
authors.initials: H
authors.lastname: Selby
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Deena M A
authors.initials: DM
authors.lastname: Gendoo
authors.affiliation: Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Grossmann
authors.affiliation: Beth Israel Deaconess Medical Center, Boston, MA, USA.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Beck
authors.affiliation: Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
authors.forename: Hugo J W L
authors.initials: HJ
authors.lastname: Aerts
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium, Ontario Institute of Cancer Research, Toronto, ON, Canada.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Lupien
authors.affiliation: Hospital for Sick Children, Toronto, ON, Canada and Department of Computer Science, University of Toronto, Toronto, ON, Canada.
authors.forename: Anna
authors.initials: A
authors.lastname: Goldenberg
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
mesh_terms: D023281:Genomics; D006801:Humans; D009369:Neoplasms; D010597:Pharmacogenetics; D011381:Programming Languages; D012984:Software