CIMICE
This is thereleased version of CIMICE; for the devel version, seeCIMICE.
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Bioconductor version: Release (3.22)
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("CIMICE")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CIMICE")For older versions of R, please refer to the appropriateBioconductor 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 | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CIMICE_1.18.0.tar.gz |
| Windows Binary (x86_64) | CIMICE_1.18.0.zip |
| macOS Binary (x86_64) | CIMICE_1.18.0.tgz |
| macOS Binary (arm64) | CIMICE_1.18.0.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 |