Design of the TRONCO bioconductor package for TRanslational ONCOlogy

Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bhubaneswar Mishra, Daniele Ramazzotti

Research output: Contribution to journalArticle

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 http://www.bioconductor.org/ under GPL license; project hosted at http://bimib.disco.unimib.it/ and https://github.com/BIMIB-DISCo/TRONCO.

Original languageEnglish (US)
Pages (from-to)39-59
Number of pages21
JournalR Journal
Volume8
Issue number2
StatePublished - 2016

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Oncology
Cancer
Progression
Model
Graphical Models
Confidence
Genomics
Mutation
Availability
Design
Series
Modeling

ASJC Scopus subject areas

  • Statistics and Probability
  • Numerical Analysis
  • Statistics, Probability and Uncertainty

Cite this

Antoniotti, M., Caravagna, G., De Sano, L., Graudenzi, A., Mauri, G., Mishra, B., & Ramazzotti, D. (2016). Design of the TRONCO bioconductor package for TRanslational ONCOlogy. R Journal, 8(2), 39-59.

Design of the TRONCO bioconductor package for TRanslational ONCOlogy. / Antoniotti, Marco; Caravagna, Giulio; De Sano, Luca; Graudenzi, Alex; Mauri, Giancarlo; Mishra, Bhubaneswar; Ramazzotti, Daniele.

In: R Journal, Vol. 8, No. 2, 2016, p. 39-59.

Research output: Contribution to journalArticle

Antoniotti, M, Caravagna, G, De Sano, L, Graudenzi, A, Mauri, G, Mishra, B & Ramazzotti, D 2016, 'Design of the TRONCO bioconductor package for TRanslational ONCOlogy', R Journal, vol. 8, no. 2, pp. 39-59.
Antoniotti M, Caravagna G, De Sano L, Graudenzi A, Mauri G, Mishra B et al. Design of the TRONCO bioconductor package for TRanslational ONCOlogy. R Journal. 2016;8(2):39-59.
Antoniotti, Marco ; Caravagna, Giulio ; De Sano, Luca ; Graudenzi, Alex ; Mauri, Giancarlo ; Mishra, Bhubaneswar ; Ramazzotti, Daniele. / Design of the TRONCO bioconductor package for TRanslational ONCOlogy. In: R Journal. 2016 ; Vol. 8, No. 2. pp. 39-59.
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