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CIMICE

This is the development version of CIMICE; for the stable release version, see CIMICE.

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


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CIMICE")

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

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 PDF
NEWS Text

Details

biocViews BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Depends
Imports dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix
System Requirements
URL https://github.com/redsnic/CIMICE
Bug Reports https://github.com/redsnic/CIMICE/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, webshot
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CIMICE_1.11.0.tar.gz
Windows Binary CIMICE_1.11.0.zip
macOS Binary (x86_64) CIMICE_1.11.0.tgz
macOS Binary (arm64) CIMICE_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CIMICE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CIMICE
Bioc Package Browser https://code.bioconductor.org/browse/CIMICE/
Package Short Url https://bioconductor.org/packages/CIMICE/
Package Downloads Report Download Stats