TRONCO
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see TRONCO.
TRONCO, an R package for TRanslational ONCOlogy
Bioconductor version: 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 gmail.com>
citation("TRONCO")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| 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 | ||
| NEWS | Text |
Details
| 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) (9.5 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 |
| System Requirements | |
| URL | https://sites.google.com/site/troncopackage/ |
| Bug Reports | https://github.com/BIMIB-DISCo/TRONCO |
See More
| Suggests | BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TRONCO_2.36.0.tar.gz |
| Windows Binary (x86_64) | TRONCO_2.36.0.zip |
| macOS Binary (x86_64) | TRONCO_2.36.0.tgz |
| macOS Binary (arm64) | TRONCO_2.36.0.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 |