The R Journal: article published in 2016, volume 8:2

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy
Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra and Daniele Ramazzotti , The R Journal (2016) 8:2, pages 39-59.

Abstract 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 patients (cross-sectional data) have been defined in the literature since late the 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 series 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 under GPL license; project hosted at and Contact.

Received: 2015-10-22; online 2016-10-21
Bioconductor packages: TRONCO

CC BY 4.0
This article is licensed under a Creative Commons Attribution 3.0 Unported license .

  author = {Marco Antoniotti and Giulio Caravagna and Luca De Sano
          and Alex Graudenzi and Giancarlo Mauri and Bud Mishra and
          Daniele Ramazzotti},
  title = {{Design of the TRONCO BioConductor Package for TRanslational
  year = {2016},
  journal = {{The R Journal}},
  url = {},
  pages = {39--59},
  volume = {8},
  number = {2}