CIMICE
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CIMICE.
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Bioconductor version: 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("CIMICE")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, GraphAndNetwork, NetworkInference, Phylogenetics, ResearchField, SingleCell, Software, StatisticalMethod, Technology |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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 |
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_1.12.0.tar.gz |
| Windows Binary (x86_64) | CIMICE_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | CIMICE_1.12.0.tgz |
| macOS Binary (arm64) | CIMICE_1.12.0.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 |