  Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R
package that implements the state-of-the-art algorithms for the inference of
cancer progression models from (epi)genomic mutational profiles. TRONCO can be
used to extract population-level models describing the trends of accumulation
of alterations in a cohort of cross-sectional samples, e.g., retrieved from
publicly available databases, and individual-level models that reveal the
clonal evolutionary history in single cancer patients, when multiple samples,
e.g., multiple biopsies or single-cell sequencing data, are available. The
resulting models can provide key hints in uncovering the evolutionary
trajectories of cancer, especially for precision medicine or personalized
therapy.
  Availability: TRONCO is released under the GPL license, it is hosted in the
Software section at http://bimib.disco.unimib.it/ and archived also at
bioconductor.org.
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