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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 (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TRONCO")

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

Documentation

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

browseVignettes("TRONCO")
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
NEWS Text

Details

biocViews Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, SingleCell, Software, SomaticMutation
Version 2.33.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 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
Linking To
Suggests BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick
System Requirements
Enhances
URL https://sites.google.com/site/troncopackage/
Bug Reports https://github.com/BIMIB-DISCo/TRONCO
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package TRONCO_2.33.0.tar.gz
Windows Binary TRONCO_2.33.0.zip
macOS Binary (x86_64) TRONCO_2.33.0.tgz
macOS Binary (arm64) TRONCO_2.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TRONCO
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TRONCO
Bioc Package Browser https://code.bioconductor.org/browse/TRONCO/
Package Short Url https://bioconductor.org/packages/TRONCO/
Package Downloads Report Download Stats