DESCRIPTION

Package: CIMICE
Type: Package
Title: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Version: 1.3.1
Authors@R: 
    c(
        person("Nicolò", "Rossi",
            role=c("aut", "cre"), email="olocin.issor@gmail.com",
            comment = c("Lab. of Computational Biology and Bioinformatics, Department of Mathematics, Computer Science and Physics, University of Udine",ORCID = "0000-0002-6353-7396"))
    )
Description: 
    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.
License: Artistic-2.0
Encoding: UTF-8
Imports: 
    dplyr,
    ggplot2,
    glue,
    tidyr,
    igraph,
    networkD3,
    visNetwork,
    ggcorrplot, 
    purrr,
    ggraph, 
    stats,
    utils,
    maftools,
    assertthat,
    tidygraph,
    expm,
    Matrix
RoxygenNote: 7.1.2
VignetteBuilder: knitr
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    webshot
biocViews: 
    Software,
    BiologicalQuestion,
    NetworkInference,
    ResearchField,
    Phylogenetics,
    StatisticalMethod,
    GraphAndNetwork,
    Technology,
    SingleCell
BugReports: https://github.com/redsnic/CIMICE/issues
URL: https://github.com/redsnic/CIMICE
BiocType: Software