DOI: 10.18129/B9.bioc.TRONCO    

This is the development version of TRONCO; for the stable release version, see TRONCO.

TRONCO, an R package for TRanslational ONCOlogy

Bioconductor version: Development (3.7)

The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).

Author: Marco Antoniotti [ctb], Giulio Caravagna [aut, cre], Luca De Sano [aut], Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut]

Maintainer: BIMIB Group <tronco at>

Citation (from within R, enter citation("TRONCO")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script An R Package for TRanslational ONCOlogy
PDF   Reference Manual
Text   NEWS


biocViews Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, Network, NetworkInference, SingleCell, Software, SomaticMutation
Version 2.11.0
In Bioconductor since BioC 3.1 (R-3.2) (3 years)
License file LICENSE
Depends R (>= 3.4)
Imports bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, gRapHD, grDevices, graphics, stats, utils, methods
Suggests BiocGenerics, BiocStyle, testthat, knitr
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TRONCO_2.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) TRONCO_2.11.0.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: