TY - JOUR T1 - Design of the TRONCO BioConductor Package for TRanslational ONCOlogy JF - bioRxiv DO - 10.1101/027524 SP - 027524 AU - Marco Antoniotti AU - Giulio Caravagna AU - Luca De Sano AU - Alex Graudenzi AU - Giancarlo Mauri AU - Bud Mishra AU - Daniele Ramazzotti Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/10/22/027524.abstract N2 - Models of cancer progression provide insights on the order of accumulation of genetic alterations during cancer development. Algorithms to infer such models from the currently available mutational profiles collected from different cancer patiens (cross-sectional data) have been defined in the literature since late 90s. These algorithms differ in the way they extract a graphical model of the events modelling the progression, e.g., somatic mutations or copy-number alterations.TRONCO is an R package for TRanslational ONcology which provides a serie of functions to assist the user in the analysis of cross-sectional genomic data and, in particular, it implements algorithms that aim to model cancer progression by means of the notion of selective advantage. These algorithms are proved to outperform the current state-of-the-art in the inference of cancer progression models. TRONCO also provides functionalities to load input cross-sectional data, set up the execution of the algorithms, assess the statistical confidence in the results and visualize the models.Availability. Freely available at http://www.bioconductor.org/ under GPL license; project hosted at http://bimib.disco.unimib.it/ and https://github.com/BIMIB-DISCo/TRONCO.Contact. tronco{at}disco.unimib.it ER -