CIMICE

DOI: 10.18129/B9.bioc.CIMICE    

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

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
License Artistic-2.0
Depends
Imports dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, relations, maftools, assertthat, 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_1.2.0.tar.gz
Windows Binary CIMICE_1.2.0.zip
macOS 10.13 (High Sierra) CIMICE_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CIMICE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CIMICE
Package Short Url https://bioconductor.org/packages/CIMICE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: