Package: ClonalSim
Type: Package
Title: Simulation of Tumor Clonal Evolution with Realistic Sequencing
        Noise
Version: 1.0.0
Authors@R: c(
    person("Gabriele", "Bucci", email = "bucci.g@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9838-7204"))
    )
Description: ClonalSim generates realistic mutational profiles of tumor samples
    with hierarchical clonal structure. It simulates founder, shared, and private
    mutations with biologically realistic noise models including intra-tumor
    heterogeneity (Beta distribution) and technical sequencing noise (negative
    binomial depth variation, binomial read sampling, base errors). The package
    is designed for benchmarking variant callers, testing clonal deconvolution
    algorithms, and teaching tumor heterogeneity concepts.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.6.0)
Imports: methods, stats, utils, ggplot2, tidyr, rlang, GenomicRanges,
        IRanges, S4Vectors, VariantAnnotation
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
biocViews: Software, Sequencing, SomaticMutation, VariantDetection,
        Coverage, Visualization, DataImport
VignetteBuilder: knitr
RoxygenNote: 7.3.3
BugReports: https://github.com/gbucci/ClonalSim/issues
URL: https://github.com/gbucci/ClonalSim
git_url: https://git.bioconductor.org/packages/ClonalSim
git_branch: RELEASE_3_23
git_last_commit: fb76c2b
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 21:16:42 UTC; biocbuild
Author: Gabriele Bucci [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9838-7204>)
Maintainer: Gabriele Bucci <bucci.g@gmail.com>
