TRONCO

Package: TRONCO
Version: 2.4.2
Date: 2016-03-23
Title: TRONCO, an R package for TRanslational ONCOlogy
Authors@R: c(person("Marco", "Antoniotti", role=c("ctb")),
person("Giulio", "Caravagna", role=c("aut", "cre"), email="giulio.caravagna@disco.unimib.it"),
person("Luca", "De Sano", role=c("aut"), email="l.desano@campus.unimib.it"),
person("Alex", "Graudenzi", role=c("aut"), email="alex.graudenzi@disco.unimib.it"),
person("Giancarlo", "Mauri", role=c("ctb")),
person("Bud", "Mishra", role=c("ctb")),
person("Daniele", "Ramazzotti", role=c("aut"), email="daniele.ramazzotti@disco.unimib.it"))
Maintainer: BIMIB Group <tronco@disco.unimib.it>
Depends: R (>= 3.3),
Imports: bnlearn, Rgraphviz, parallel, foreach, doParallel, iterators,
RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable,
gtable, scales, R.matlab, gRapHD, infotheo, grDevices,
graphics, stats, utils,
Suggests: BiocGenerics, BiocStyle, testthat, knitr,
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.
Encoding: UTF-8
LazyData: TRUE
License: file LICENSE
URL: https://sites.google.com/site/troncopackage/
BugReports: https://github.com/BIMIB-DISCo/TRONCO
biocViews: BiomedicalInformatics, Bayesian, GraphAndNetwork,
SomaticMutation, NetworkInference, Network, Clustering,
DataImport
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:09:24 UTC; biocbuild
Author: Marco Antoniotti [ctb],
Giulio Caravagna [aut, cre],
Luca De Sano [aut],
Alex Graudenzi [aut],
Giancarlo Mauri [ctb],
Bud Mishra [ctb],
Daniele Ramazzotti [aut]

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TRONCO' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TRONCO'
    finding HTML links ... done
    AND                                     html  
    OR                                      html  
    TCGA.map.clinical.data                  html  
    TCGA.multiple.samples                   html  
    TCGA.remove.multiple.samples            html  
    TCGA.shorten.barcodes                   html  
    XOR                                     html  
    aCML                                    html  
    annotate.description                    html  
    annotate.stages                         html  
    as.adj.matrix                           html  
    as.alterations                          html  
    as.bootstrap.scores                     html  
    as.colors                               html  
    as.conditional.probs                    html  
    as.confidence                           html  
    as.description                          html  
    as.events                               html  
    as.events.in.patterns                   html  
    as.events.in.sample                     html  
    as.gene                                 html  
    as.genes                                html  
    as.genes.in.patterns                    html  
    as.genotypes                            html  
    as.hypotheses                           html  
    as.joint.probs                          html  
    as.kfold.eloss                          html  
    as.kfold.posterr                        html  
    as.kfold.prederr                        html  
    as.marginal.probs                       html  
    as.models                               html  
    as.parameters                           html  
    as.pathway                              html  
    as.patterns                             html  
    as.samples                              html  
    as.selective.advantage.relations        html  
    as.stages                               html  
    as.types                                html  
    as.types.in.patterns                    html  
    cbio.query                              html  
    change.color                            html  
    consolidate.data                        html  
    crc_gistic                              html  
    crc_maf                                 html  
    crc_plain                               html  
    delete.event                            html  
    delete.gene                             html  
    delete.hypothesis                       html  
    delete.model                            html  
    delete.pattern                          html  
    delete.samples                          html  
    delete.type                             html  
    duplicates                              html  
    ebind                                   html  
    enforce.numeric                         html  
    enforce.string                          html  
    events.selection                        html  
    export.graphml                          html  
    export.mutex                            html  
    export.nbs.input                        html  
    extract.MAF.HuGO.Entrez.map             html  
    genes.table.report                      html  
    has.duplicates                          html  
    has.model                               html  
    has.stages                              html  
    hypothesis.add                          html  
    hypothesis.add.group                    html  
    hypothesis.add.homologous               html  
    import.GISTIC                           html  
    import.MAF                              html  
    import.genotypes                        html  
    import.mutex.groups                     html  
    intersect.datasets                      html  
    is.compliant                            html  
    join.events                             html  
    join.types                              html  
    keysToNames                             html  
    maf                                     html  
    muts                                    html  
    nameToKey                               html  
    nevents                                 html  
    ngenes                                  html  
    nhypotheses                             html  
    npatterns                               html  
    nsamples                                html  
    ntypes                                  html  
    oncoprint                               html  
    oncoprint.cbio                          html  
    order.frequency                         html  
    pathway.visualization                   html  
    pheatmap                                html  
    rank.recurrents                         html  
    rename.gene                             html  
    rename.type                             html  
    samples.selection                       html  
    sbind                                   html  
    ssplit                                  html  
    stage                                   html  
    test_dataset                            html  
    test_dataset_no_hypos                   html  
    test_model                              html  
    test_model_kfold                        html  
    trim                                    html  
    tronco.bootstrap                        html  
    tronco.caprese                          html  
    tronco.capri                            html  
    tronco.kfold.eloss                      html  
    tronco.kfold.posterr                    html  
    tronco.kfold.prederr                    html  
    tronco.mst.chowliu                      html  
    tronco.mst.edmonds                      html  
    tronco.mst.prim                         html  
    tronco.pattern.plot                     html  
    tronco.plot                             html  
    view                                    html  
    which.samples                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TRONCO)
Making 'packages.html' ... done