To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TRONCO")

In most cases, you don't need to download the package archive at all.

TRONCO

 

TRONCO, an R package for TRanslational ONCOlogy

Bioconductor version: Release (3.5)

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 disco.unimib.it>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TRONCO")

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
Text   LICENSE

Details

biocViews Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, Network, NetworkInference, SingleCell, Software, SomaticMutation
Version 2.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 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
LinkingTo
Suggests BiocGenerics, BiocStyle, testthat, knitr
SystemRequirements
Enhances
URL https://sites.google.com/site/troncopackage/
BugReports https://github.com/BIMIB-DISCo/TRONCO
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source TRONCO_2.8.0.tar.gz
Windows Binary TRONCO_2.8.0.zip
Mac OS X 10.11 (El Capitan) TRONCO_2.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TRONCO
Package Short Url http://bioconductor.org/packages/TRONCO/
Package Downloads Report Download Stats

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