DESCRIPTION

Package: LACE
Version: 2.10.0
Date: 2024-10-31
Title: Longitudinal Analysis of Cancer Evolution (LACE)
Authors@R: c(person("Daniele", "Ramazzotti", role=c("aut"),email="daniele.ramazzotti@unimib.it",
                comment = c(ORCID = "0000-0002-6087-2666")),
    person("Fabrizio","Angaroni",role=c("aut"),email="fabrizio.angaroni@unimib.it"),
    person("Davide","Maspero",role=c("cre","aut"),email="d.maspero@campus.unimib.it"),
    person("Alex","Graudenzi",role=c("aut"),email="alex.graudenzi@unimib.it"),
    person("Luca", "De Sano", role=c("aut"), email="luca.desano@gmail.com",
                comment = c(ORCID = "0000-0002-9618-3774")),
    person("Gianluca","Ascolani",role=c("aut"),email="gianluca.ascolani@unimib.it"))
Depends: R (>= 4.2.0)
Imports:
    curl,
    igraph,
    foreach,
    doParallel,
    sortable,
    dplyr,
    forcats,
    data.tree, 
    graphics, 
    grDevices, 
    parallel, 
    RColorBrewer, 
    Rfast, 
    stats, 
    SummarizedExperiment, 
    utils, 
    purrr, 
    stringi, 
    stringr, 
    Matrix, 
    tidyr, 
    jsonlite,
    readr,
    configr,
    DT,
    tools,
    fs,
    data.table,
    htmltools, 
    htmlwidgets,
    bsplus,
    shinyvalidate,
    shiny,
    shinythemes,
    shinyFiles,
    shinyjs,
    shinyBS,
    shinydashboard,
    biomaRt,
    callr,
    logr,
    ggplot2,
    svglite
Suggests:
    BiocGenerics,
    BiocStyle,
    testthat,
    knitr,
    rmarkdown
Name:
    LACE: an R package for the inference of longitudinal cancer evolution models
Description:
    LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/BIMIB-DISCo/LACE
BugReports: https://github.com/BIMIB-DISCo/LACE
biocViews:
    BiomedicalInformatics, 
    SingleCell, 
    SomaticMutation
RoxygenNote: 7.3.2
VignetteBuilder: knitr