Package: TRONCO
Version: 2.42.0
Date: 2025-09-10
Title: TRONCO, an R package for TRanslational ONCOlogy
Authors@R: c(person("Marco", "Antoniotti", role=c("ctb")), 
    person("Giulio", "Caravagna", role=c("aut"), email="gcaravagna@units.it"),
    person("Luca", "De Sano", role=c("cre","aut"), email="luca.desano@gmail.com",
                comment = c(ORCID = "0000-0002-9618-3774")), 
    person("Alex", "Graudenzi", role=c("aut"), email="alex.graudenzi@unimib.it"),
    person("Giancarlo", "Mauri", role=c("ctb")), 
    person("Bud", "Mishra", role=c("ctb")), 
    person("Daniele", "Ramazzotti", role=c("aut"),email="daniele.ramazzotti@unimib.it",
                comment = c(ORCID = "0000-0002-6087-2666")))
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
Name: An R package for the inference of cancer progression models from
        heterogeneous genomic data
Description: 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).
Encoding: UTF-8
License: GPL-3
URL: https://sites.google.com/site/troncopackage/
BugReports: https://github.com/BIMIB-DISCo/TRONCO
biocViews: BiomedicalInformatics, Bayesian, GraphAndNetwork,
        SomaticMutation, NetworkInference, Network, Clustering,
        DataImport, SingleCell, ImmunoOncology
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:23:30 UTC
RemoteUrl: https://github.com/bioc/TRONCO
RemoteRef: RELEASE_3_22
RemoteSha: f575cac6be6e05949e425f7143c2d939aff58880
NeedsCompilation: no
Packaged: 2026-03-04 08:02:17 UTC; root
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>)
Maintainer: Luca De Sano <luca.desano@gmail.com>
Built: R 4.5.2; ; 2026-03-04 08:03:51 UTC; windows
