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TRONCO (TRanslational ONCOlogy) =============================== [![Actions Status](]( [![Actions Status](]( | Branch | Status | | --- | --- | | master | [![R-CMD-check-bioc](]( | | development | [![R-CMD-check-bioc](]( | The **TRONCO** (*TR*anslational *ONCO*logy) **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).