This is the released version of CIMICE; for the devel version, see CIMICE.
CIMICE-R: (Markov) Chain Method to Inferr Cancer EvolutionBioconductor version: Release (3.21)
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: ORCID: 0000-0002-6353-7396 )
Maintainer: Nicolò Rossi <olocin.issor at gmail.com>
Citation (from within R, entercitation("CIMICE")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CIMICE")Follow Installation instructions to use this package in your R session.
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