TRONCO
TRONCO, an R package for TRanslational ONCOlogy
Bioconductor version: 3.23 · Package version: 2.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TRONCO")Details
| Maintainer | Luca De Sano <luca.desano@gmail.com> |
| Author | Marco Antoniotti [ctb], Giulio Caravagna [aut], Luca De Sano [cre, aut] (ORCID: <https://orcid.org/0000-0002-9618-3774>), Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut] (ORCID: <https://orcid.org/0000-0002-6087-2666>) |
| License | GPL-3 |
| URL | https://sites.google.com/site/troncopackage/ |
| Bug Reports | https://github.com/BIMIB-DISCo/TRONCO |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, BiomedicalInformatics, Clustering, DataImport, GraphAndNetwork, ImmunoOncology, Network, NetworkInference, SingleCell, Software, SomaticMutation |
| Package Short Url | https://bioconductor.org/packages/TRONCO/ |
Citation
From within R, enter citation("TRONCO"):
Giulio Caravagna, Luca De Sano, Alex Graudenzi, Daniele Ramazzotti. TRONCO: TRONCO, an R package for TRanslational ONCOlogy. doi:10.18129/B9.bioc.TRONCO, R package version 2.44.0, https://bioconductor.org/packages/TRONCO.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- An introduction to the TRONCO R package
- Data manipulation
- Data visualization
- Import/export from other tools
- Loading data
- Model inference
- Post reconstruction
Download
Follow the installation instructions to use this package in your R session.
| Source package | TRONCO_2.44.0.tar.gz |
| Windows binary (x86_64) | TRONCO_2.44.0.zip |
| macOS binary (arm64) | TRONCO_2.44.0.tgz |
| macOS binary (x86_64) | TRONCO_2.44.0.tgz |
Dependencies
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
Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick