TRONCO

DOI: 10.18129/B9.bioc.TRONCO    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TRONCO.

TRONCO, an R package for TRanslational ONCOlogy

Bioconductor version: 3.11

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: Luca De Sano <luca.desano at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

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

Details

biocViews	Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, SingleCell, Software, SomaticMutation
Version	2.20.1
In Bioconductor since	BioC 3.1 (R-3.2) (5.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods
LinkingTo
Suggests	BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways
SystemRequirements
Enhances
URL	https://sites.google.com/site/troncopackage/
BugReports	https://github.com/BIMIB-DISCo/TRONCO
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_2.20.1.tar.gz
Windows Binary	TRONCO_2.20.1.zip
macOS 10.13 (High Sierra)	TRONCO_2.20.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TRONCO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TRONCO
Package Short Url	https://bioconductor.org/packages/TRONCO/
Package Downloads Report	Download Stats