CIMICE
This is the released version of CIMICE; for the devel version, see CIMICE.
All Bioconductor versions of CIMICE
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Bioconductor version: 3.23 · Package version: 1.20.0
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, ORCID: 
)
Maintainer: Nicolò Rossi <olocin.issor at gmail.com>
Citation
From within R, enter citation("CIMICE"):
Nicolò Rossi. CIMICE: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution. doi:10.18129/B9.bioc.CIMICE, R package version 1.20.0, https://bioconductor.org/packages/CIMICE.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CIMICE")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.20.0 |
| License | Artistic-2.0 |
| URL | https://github.com/redsnic/CIMICE |
| Bug Reports | https://github.com/redsnic/CIMICE/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| Downloads rank | 1830 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology |
| Package Short Url | https://bioconductor.org/packages/CIMICE/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CIMICE")| CIMICE-R: (Markov) Chain Method to Infer Cancer Evolution | HTML | R Script |
| Quick guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CIMICE_1.20.0.tar.gz |
| Windows binary (x86_64) | CIMICE_1.20.0.zip |
| macOS binary (arm64) | CIMICE_1.20.0.tgz |
| macOS binary (x86_64) | CIMICE_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CIMICE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CIMICE |
| Package Downloads Report | Download Stats |