CIMICE

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

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

Bioconductor version: Development (3.24)

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, enter citation("CIMICE")):

Nicolò Rossi. CIMICE: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution. doi:10.18129/B9.bioc.CIMICE, R package version 1.21.0, https://bioconductor.org/packages/CIMICE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology
Version	1.21.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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

Suggests	BiocStyle, knitr, rmarkdown, testthat, webshot
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	CIMICE_1.21.0.tar.gz
Windows Binary (x86_64)	CIMICE_1.21.0.zip
macOS Binary (big-sur-x86_64)	CIMICE_1.21.0.tgz
macOS Binary (sonoma-arm64)	CIMICE_1.21.0.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