Name Mode Size
..
2022-03-12 040000
README.md
# CIMICE-R 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. See [this repository](https://github.com/redsnic/tumorEvolutionWithMarkovChains/tree/master/GenotypeEvolutionPaths) for the original Java version of this tool. ### Installation from GitHub: ```{R} # install package devtools::install_github("redsnic/CIMICE", build_vignettes = TRUE, dependencies = TRUE) library(CIMICE) # simple example quick_run(example_dataset()) # show guide browseVignettes("CIMICE") ``` remember to install [**pandoc**](https://pandoc.org/installing.html) to build the vignettes. ### Input Formats: #### CAPRI format ``` s/g gene_1 gene_2 ... gene_n sample_1 1 0 ... 0 ... sample_m 1 1 ... 1 ``` #### CAPRIpop format ``` s/g gene_1 gene_2 ... gene_n freq sample_1 1 0 ... 0 freq_s1 ... sample_m 1 1 ... 1 freq_sm ``` (With this format, feature selection for most mutated samples or genes is disabled in the web application) ### Web Application: A simple `shiny` web application to use CIMICE is available [here](https://redsnic.shinyapps.io/CIMICE_WEB/).