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 for the original Java version of this tool.

Installation from GitHub:

# 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 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.