{ "_id": "6a1aeb911d7bb097a09f3f12", "Package": "TRONCO", "Version": "2.45.0", "Date": "2026-03-09", "Title": "TRONCO, an R package for TRanslational ONCOlogy", "Authors@R": "c(person(\"Marco\", \"Antoniotti\", role=c(\"ctb\")), \nperson(\"Giulio\", \"Caravagna\", role=c(\"aut\"), email=\"gcaravagna@units.it\"),\nperson(\"Luca\", \"De Sano\", role=c(\"cre\",\"aut\"), email=\"luca.desano@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9618-3774\")),\nperson(\"Alex\", \"Graudenzi\", role=c(\"aut\"), email=\"alex.graudenzi@unimib.it\"),\nperson(\"Giancarlo\", \"Mauri\", role=c(\"ctb\")),\nperson(\"Bud\", \"Mishra\", role=c(\"ctb\")),\nperson(\"Daniele\", \"Ramazzotti\", role=c(\"aut\"),email=\"daniele.ramazzotti@unimib.it\",\ncomment = c(ORCID = \"0000-0002-6087-2666\")))", "Name": "An R package for the inference of cancer progression models from\nheterogeneous genomic data", "Description": "The TRONCO (TRanslational ONCOlogy) R package collects\nalgorithms to infer progression models via the approach of\nSuppes-Bayes Causal Network, both from an ensemble of tumors\n(cross-sectional samples) and within an individual patient\n(multi-region or single-cell samples). The package provides\nparallel implementation of algorithms that process binary\nmatrices where each row represents a tumor sample and each\ncolumn a single-nucleotide or a structural variant driving the\nprogression; a 0/1 value models the absence/presence of that\nalteration in the sample. The tool can import data from plain,\nMAF or GISTIC format files, and can fetch it from the\ncBioPortal for cancer genomics. Functions for data manipulation\nand visualization are provided, as well as functions to\nimport/export such data to other bioinformatics tools for, e.g,\nclustering or detection of mutually exclusive alterations.\nInferred models can be visualized and tested for their\nconfidence via bootstrap and cross-validation. TRONCO is used\nfor the implementation of the Pipeline for Cancer Inference\n(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,\nSomaticMutation, NetworkInference, Network, Clustering,\nDataImport, SingleCell, ImmunoOncology", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:23 UTC", "RemoteUrl": "https://github.com/bioc/TRONCO", "RemoteRef": "HEAD", "RemoteSha": "652830a9fc60f70ca986b2b7f2da5c0144b8c4ef", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:40:15 UTC", "User": "root" }, "Author": "Marco Antoniotti [ctb],\nGiulio Caravagna [aut],\nLuca De Sano [cre, aut] (ORCID:\n),\nAlex Graudenzi [aut],\nGiancarlo Mauri [ctb],\nBud Mishra [ctb],\nDaniele 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"maf", "title": "MAF example data", "topics": [ "maf" ] }, { "page": "muts", "title": "Simple mutation dataset", "topics": [ "muts" ] }, { "page": "nameToKey", "title": "nameToKey", "topics": [ "nameToKey" ] }, { "page": "nevents", "title": "nevents", "topics": [ "nevents" ] }, { "page": "ngenes", "title": "ngenes", "topics": [ "ngenes" ] }, { "page": "nhypotheses", "title": "Return the number of hypotheses in the dataset", "topics": [ "nhypotheses" ] }, { "page": "npatterns", "title": "Return the number of patterns in the dataset", "topics": [ "npatterns" ] }, { "page": "nsamples", "title": "nsamples", "topics": [ "nsamples" ] }, { "page": "ntypes", "title": "ntypes", "topics": [ "ntypes" ] }, { "page": "oncoprint", "title": "oncoprint", "topics": [ "oncoprint" ] }, { "page": "oncoprint.cbio", "title": "oncoprint.cbio", "topics": [ "oncoprint.cbio" ] }, { "page": "OR", "title": "OR", "topics": [ "OR" ] }, { "page": "order.frequency", "title": "order.frequency", "topics": [ "order.frequency" ] }, { "page": "pathway.visualization", "title": "pathway.visualization", "topics": [ "pathway.visualization" ] }, { "page": "pheatmap", "title": "A function to draw clustered heatmaps.", "topics": [ "pheatmap" ] }, { "page": "rank.recurrents", "title": "rank.recurrents", "topics": [ "rank.recurrents" ] }, { "page": "rename.gene", "title": "rename.gene", "topics": [ "rename.gene" ] }, { "page": "rename.type", "title": "rename.type", "topics": [ "rename.type" ] }, { "page": "samples.selection", "title": "samples.selection", "topics": [ "samples.selection" ] }, { "page": "sbind", "title": "sbind", "topics": [ "sbind" ] }, { "page": "ssplit", "title": "ssplit", "topics": [ "ssplit" ] }, { "page": "stage", "title": "Stage information for test_dataset", "topics": [ "stage" ] }, { "page": "TCGA.map.clinical.data", "title": "TCGA.map.clinical.data", "topics": [ "TCGA.map.clinical.data" ] }, { "page": "TCGA.multiple.samples", "title": "TCGA.multiple.samples", "topics": [ "TCGA.multiple.samples" ] }, { "page": "TCGA.remove.multiple.samples", "title": "TCGA.remove.multiple.samples", "topics": [ "TCGA.remove.multiple.samples" ] }, { "page": "TCGA.shorten.barcodes", "title": "TCGA.shorten.barcodes", "topics": [ "TCGA.shorten.barcodes" ] }, { "page": "test_dataset", "title": "A complete dataset with hypotheses", "topics": [ "test_dataset" ] }, { "page": "test_dataset_no_hypos", "title": "A complete dataset", "topics": [ "test_dataset_no_hypos" ] }, { "page": "test_model", "title": "A complete dataset with a reconstructed model", "topics": [ "test_model" ] }, { "page": "test_model_kfold", "title": "A complete dataset with a reconstructed model and crossvalidation informations", "topics": [ "test_model_kfold" ] }, { "page": "trim", "title": "trim", "topics": [ "trim" ] }, { "page": "tronco.bootstrap", "title": "tronco bootstrap", "topics": [ "tronco.bootstrap" ] }, { "page": "tronco.caprese", "title": "tronco caprese", "topics": [ "tronco.caprese" ] }, { "page": "tronco.capri", "title": "tronco capri", "topics": [ "tronco.capri" ] }, { "page": "tronco.chowliu", "title": "Tronco Chow Liu", "topics": [ "tronco.chowliu" ] }, { "page": "tronco.edmonds", "title": "Tronco Edmonds", "topics": [ "tronco.edmonds" ] }, { "page": "tronco.gabow", "title": "Tronco Gabow", "topics": [ "tronco.gabow" ] }, { "page": "tronco.kfold.eloss", "title": "tronco.kfold.eloss", "topics": [ "tronco.kfold.eloss" ] }, { "page": "tronco.kfold.posterr", "title": "tronco.kfold.posterr. For details and examples regarding the statistical assesment of an inferred model, we refer to the Vignette Section 7.", "topics": [ "tronco.kfold.posterr" ] }, { "page": "tronco.kfold.prederr", "title": "tronco.kfold.prederr", "topics": [ "tronco.kfold.prederr" ] }, { "page": "tronco.pattern.plot", "title": "tronco.pattern.plot", "topics": [ "tronco.pattern.plot" ] }, { "page": "tronco.plot", "title": "tronco.plot", "topics": [ "tronco.plot" ] }, { "page": "tronco.prim", "title": "Tronco Prim", "topics": [ "tronco.prim" ] }, { "page": "view", "title": "view", "topics": [ "view" ] }, { "page": "which.samples", "title": "which.samples", "topics": [ "which.samples" ] }, { "page": "XOR", "title": "XOR", "topics": [ "XOR" ] } ], "_readme": "https://github.com/bioc/TRONCO/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "bnlearn", "circlize", "cli", "codetools", "colorspace", "cpp11", "doParallel", "farver", "foreach", "generics", "GlobalOptions", "glue", "graph", "gridExtra", "gtable", "gtools", "igraph", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "R.matlab", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rgraphviz", "rlang", "scales", "shape", "vctrs", "viridisLite", "xtable" ], "_vignettes": [ { "source": "f1_introduction.rmd", "filename": "f1_introduction.html", "title": "An introduction to the TRONCO R package", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Changelog", "Algorithms and useful links", "External links to resources related to TRONCO" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f4_data_manipulation.Rmd", "filename": "f4_data_manipulation.html", "title": "Data manipulation", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Modifying events and samples", "Modifying patterns", "Subsetting a dataset" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f3_data_visualization.Rmd", "filename": "f3_data_visualization.html", "title": "Data visualization", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Summary report for a dataset and boolean queries", "Creating views with the as functions", "Dataset size", "Oncoprints", "Groups visualization (e.g., pathways)" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f7_import_export.Rmd", "filename": "f7_import_export.html", "title": "Import/export from other tools", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f2_loading_data.Rmd", "filename": "f2_loading_data.html", "title": "Loading data", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Preliminaries", "Mutations annotated in a MAF format", "Copy Number Variants annotated in the GISTIC format", "Custom alterations annotated in a boolean matrix", "Downloading data from the cBio portal for cancer genomics" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f5_model_inference.Rmd", "filename": "f5_model_inference.html", "title": "Model inference", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Data consolidation.", "CAPRI", "Testable hypotheses via logical formulas (i.e., patterns)", "Adding custom hypotheses.", "Adding (automatically) hypotheses for homologous events.", "Adding (automatically) hypotheses for a group of genes.", "Querying, visualizing and manipulating CAPRI's patterns.", "How to build a pattern.", "Model reconstruction", "CAPRESE", "Directed Minimum Spanning Tree with Mutual Information", "Partially Directed Minimum Spanning Tree with Mutual Information", "Undirected Minimum Spanning Tree with Likelihood-Fit", "Undirected Minimum Spanning Tree with Mutual Information" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 }, { "source": "f6_post_reconstruction.Rmd", "filename": "f6_post_reconstruction.html", "title": "Post reconstruction", "author": "Luca De Sano, Daniele Ramazzotti, Giulio Caravagna, Alex Graudenxi, Marco Antoniotti", "engine": "knitr::rmarkdown", "headings": [ "Visualizing a reconstructed model", "Accessing information within a model (e.g., confidence)", "Model structure", "Empirical probabilities", "Confidence measures", "Confidence via non-parametric and statistical bootstrap", "Confidence via cross-validation (entropy loss, prediction and posterior classification errors)" ], "created": "2023-04-05 10:43:38", "modified": "2024-09-29 19:39:38", "commits": 2 } ], "_score": 8.39262661647404, "_indexed": true, "_nocasepkg": "tronco", "_universes": [ "bioc", "luca-dex", "bimib-disco" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.45.0", "date": "2026-05-30T10:02:06.000Z", "distro": "noble", "commit": "652830a9fc60f70ca986b2b7f2da5c0144b8c4ef", "fileid": "1c501ec0d73b6eb7e22e73fcc67e6ba1051f4805ed3267c83a684f7809a17cc1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676374207" }, { "r": "4.6.0", "os": "linux", "version": "2.45.0", "date": "2026-05-30T10:02:04.000Z", "distro": "noble", "commit": "652830a9fc60f70ca986b2b7f2da5c0144b8c4ef", "fileid": "66fdd2b7fc965631e2df16ca8deaec60417ea9e7fb4502ff53c9e7cdd0d0c5b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676374207" }, { "r": 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