Cimice

R implementation of the CIMICE tool. CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction. See ‘https://github.com/redsnic/tumorEvolutionWithMarkovChains/tree/master/GenotypeEvolutionPaths' for the original Java version of this tool.

See Cimice’s home page.