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TRONCO, an R package for TRanslational ONCOlogy

Bioconductor version: Release (3.19)

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], Luca De Sano [cre, aut] , Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut]

Maintainer: Luca De Sano <luca.desano at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

Data manipulation HTML R Script
Data visualization HTML R Script
f1_introduction.html HTML R Script
Import/export from other tools HTML R Script
Loading data HTML R Script
Model inference HTML R Script
Post reconstruction HTML R Script
Reference Manual PDF


biocViews Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, SingleCell, Software, SomaticMutation
Version 2.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-3
Depends R (>= 4.1.0)
Imports bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods
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Source Package TRONCO_2.36.0.tar.gz
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macOS Binary (arm64) TRONCO_2.36.0.tgz
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