TRONCO

DOI:10.18129/B9.bioc.TRONCO

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, seeTRONCO.

TRONCO, an R package for TRanslational ONCOlogy

Bioconductor version: 3.10

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

Citation (from within R, entercitation("TRONCO")):

Installation

To install this package, start R (version "3.6") and enter:

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

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

Documentation

查看文档的版本包age 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 2.18.0
In Bioconductor since BioC 3.1 (R-3.2) (5 years)
License GPL-3
Depends R (>= 3.6)
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

Followbob 体育网址 instructions to use this package in your R session.

Source Package TRONCO_2.18.0.tar.gz
Windows Binary TRONCO_2.18.0.zip(32- & 64-bit)
Mac OS X 10.11 (El Capitan) TRONCO_2.18.0.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 //www.anjoumacpherson.com/packages/TRONCO/
Package Downloads Report Download Stats

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