Package: ClonalSim
Type: Package
Title: Simulation of Tumor Clonal Evolution with Realistic Sequencing
        Noise
Version: 1.1.0
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 (>= 4.5.0)
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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:07:19 UTC
RemoteUrl: https://github.com/bioc/ClonalSim
RemoteRef: HEAD
RemoteSha: 6048f4bf99d8d4830dcc714f9cf298ed72c22269
NeedsCompilation: no
Packaged: 2026-05-29 08:18:29 UTC; root
Author: Gabriele Bucci [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9838-7204>)
Maintainer: Gabriele Bucci <bucci.g@gmail.com>