CIMICE
This is the development version of CIMICE; for the stable release version, see CIMICE.
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:
)
Maintainer: Nicolò Rossi <olocin.issor at gmail.com>
citation("CIMICE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 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 | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_1.21.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/CIMICE/ |
| Package Short Url | https://bioconductor.org/packages/CIMICE/ |
| Package Downloads Report | Download Stats |