title: regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
abstract: BACKGROUND
  Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model.
  
  
  CONCLUSIONS
  regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association.
  
  
  METHODS
  regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR).
  
  
  BACKGROUND
  rmalinverni@carrerasresearch.org.
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
authors.forename: Bernat
authors.initials: B
authors.lastname: Gel
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
authors.forename: Anna
authors.initials: A
authors.lastname: Díez-Villanueva
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
authors.forename: Eduard
authors.initials: E
authors.lastname: Serra
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and Josep Carreras Institute for Leukaemia Research (IJC), Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain.
authors.forename: Marcus
authors.initials: M
authors.lastname: Buschbeck
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Peinado
authors.affiliation: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain and.
authors.forename: Roberto
authors.initials: R
authors.lastname: Malinverni
mesh_terms: D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software