ClonalSim
This is the development version of ClonalSim; for the stable release version, see ClonalSim.
All Bioconductor versions of ClonalSim
3.24 (devel), 3.23 (release)
Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise
Bioconductor version: 3.24 · Package version: 1.1.0
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.
Author: Gabriele Bucci [aut, cre] 
Maintainer: Gabriele Bucci <bucci.g at gmail.com>
Citation
From within R, enter citation("ClonalSim"):
Gabriele Bucci. ClonalSim: Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise. doi:10.18129/B9.bioc.ClonalSim, R package version 1.1.0, https://bioconductor.org/packages/ClonalSim.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ClonalSim")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/gbucci/ClonalSim |
| Bug Reports | https://github.com/gbucci/ClonalSim/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2311 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, DataImport, Sequencing, Software, SomaticMutation, VariantDetection, Visualization |
| Package Short Url | https://bioconductor.org/packages/ClonalSim/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ClonalSim")| Introduction to ClonalSim | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ClonalSim_1.1.0.tar.gz |
| Windows binary (x86_64) | ClonalSim_1.1.0.zip |
| macOS binary (arm64) | ClonalSim_1.1.0.tgz |
| macOS binary (x86_64) | ClonalSim_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClonalSim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClonalSim |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: methods, stats, utils, ggplot2, tidyr, rlang, GenomicRanges, IRanges, S4Vectors, VariantAnnotation
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle