DESCRIPTION

Package: SelectSim
Title: Selected Events Linked by Evolutionary Conditions in Cancer
Version: 0.1.6
Authors@R: c(
    person("Arvind", "Iyer", , "ayalurarvind@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8247-700X")),
    person("Marco", "Mina", , "marco.mina.85@gmail.com", role = "aut"),
    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = c("aut", "cph")),
    person("Giovanni", "Ciriello", , "giovanni.ciriello@unil.ch", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0003-2021-8683"))
  )
Description: Implements the 'SelectSim' methodology for identifying patterns of
    co-occurrence and mutual exclusivity between functional genomic alterations
    in cancer cohorts. The package processes mutation annotation data, constructs
    alteration matrices, estimates expected alteration-pair frequencies, and
    quantifies deviations associated with selective interactions. The methodology
    is described in Iyer et al. (2026) <doi:10.1038/s41588-026-02661-4>.
License: MIT + file LICENSE
URL: https://csogroup.github.io/SelectSim/
BugReports: https://github.com/CSOgroup/SelectSim/issues
Depends:
    R (>= 3.5)
Imports:
    doParallel,
    doRNG,
    dplyr,
    foreach,
    ggplot2,
    ggpubr,
    ggridges,
    Matrix,
    parallel,
    Rcpp,
    Rfast,
    stats
Suggests:
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    tictoc
LinkingTo:
    Rcpp,
    RcppArmadillo
VignetteBuilder: 
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
Language: en-US