title: TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.
abstract: We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy.
  
  
  
  TRONCO is released under the GPL license, is hosted at http://bimib.disco.unimib.it/ (Software section) and archived also at bioconductor.org.
  
  
  
  tronco@disco.unimib.it
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca.
authors: Luca
authors: L
authors: De Sano
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca, School of Informatics, University of Edinburgh, Edinburgh, UK.
authors: Giulio
authors: G
authors: Caravagna
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca.
authors: Daniele
authors: D
authors: Ramazzotti
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca, Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Milan, Italy.
authors: Alex
authors: A
authors: Graudenzi
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca.
authors: Giancarlo
authors: G
authors: Mauri
authors: Courant Institute of Mathematical Sciences, New York University, New York, NY, USA and.
authors: Bud
authors: B
authors: Mishra
authors: Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy.
authors: Marco
authors: M
authors: Antoniotti
mesh_terms: D000465:Algorithms; D018450:Disease Progression; D044127:Epigenesis, Genetic; D023281:Genomics; D006801:Humans; D008962:Models, Theoretical; D009369:Neoplasms / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface