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

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("CIMICE")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CIMICE-R: (Markov) Chain Method to Infer Cancer Evolution HTML R Script
Quick guide HTML R Script
Reference Manual PDF


biocViews BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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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Follow Installation instructions to use this package in your R session.

Source Package CIMICE_1.12.0.tar.gz
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macOS Binary (x86_64) CIMICE_1.12.0.tgz
macOS Binary (arm64) CIMICE_1.12.0.tgz
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