Package: CIMICE
Type: Package
Title: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Version: 1.21.0
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
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libbz2-dev libicu-dev liblzma-dev libuv1-dev
        libxml2-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:26 UTC
RemoteUrl: https://github.com/bioc/CIMICE
RemoteRef: HEAD
RemoteSha: 57344c846b0a08505194acdb7fd2b6f0589d7bc8
NeedsCompilation: no
Packaged: 2026-07-03 23:40:06 UTC; root
Author: Nicolò Rossi [aut, cre] (Lab. of Computational Biology and
    Bioinformatics, Department of Mathematics, Computer Science and
    Physics, University of Udine, ORCID:
    <https://orcid.org/0000-0002-6353-7396>)
Maintainer: Nicolò Rossi <olocin.issor@gmail.com>