CIMICE

DOI: 10.18129/B9.bioc.CIMICE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CIMICE.

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

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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.

Documentation

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

browseVignettes("CIMICE")

 

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

Details

biocViews	BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Artistic-2.0
Depends
Imports	dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, webshot
SystemRequirements
Enhances
URL	https://github.com/redsnic/CIMICE
BugReports	https://github.com/redsnic/CIMICE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CIMICE_1.6.0.tar.gz
Windows Binary	CIMICE_1.6.0.zip
macOS Binary (x86_64)	CIMICE_1.6.0.tgz
macOS Binary (arm64)	CIMICE_1.6.0.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