DOI: 10.18129/B9.bioc.CIMICE  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CIMICE.

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Bioconductor version: 3.17

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.

Author: Nicolò Rossi [aut, cre] (Lab. of Computational Biology and Bioinformatics, Department of Mathematics, Computer Science and Physics, University of Udine, )

Maintainer: Nicolò Rossi <olocin.issor at>

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biocViews BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2.5 years)
License Artistic-2.0
Imports dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix
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