CIMICE

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CIMICE.

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


Bioconductor version: 3.17

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 "4.3") 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")
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 1.8.0
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
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CIMICE_1.8.0.tar.gz
Windows Binary CIMICE_1.8.0.zip
macOS Binary (x86_64) CIMICE_1.8.0.tgz
macOS Binary (arm64) CIMICE_1.8.0.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
Old Source Packages for BioC 3.17 Source Archive