TRONCO started in 2014 as a collaborative effort between a Bioinformatics unit at Milano-Bicocca (Italy) and one at New York University (USA); it provides the R implementation of a set of state-of-the-art machine learning algorithms to infer models of cancer progression from cancer genomics data. The Pipeline for Cancer Inference, PiCnIc, is a very recent software pipeline developed in 2016, which includes further collaborations from the University of Edinburgh (UK) and Stanford University (USA). PiCnIc is the first full pipeline to pre-process cancer genome data and automatize all the procedure to use TRONCO. The Cytoscape interface is a perspective tool, cyTRON, that will allow manipulating cancer data within the common platform Cytoscape, so to be able to exploit the Cytoscape well-known capabilities of integrating different type of "omics" data in a very intuitive way.
