ClonalSim
This is the released version of ClonalSim; for the devel version, see ClonalSim.
Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise
Bioconductor version: Release (3.23)
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("ClonalSim")):Gabriele Bucci. ClonalSim: Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise. doi:10.18129/B9.bioc.ClonalSim, R package version 1.0.0, 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")
BiocManager::install("ClonalSim")For older versions of R, please refer to the appropriate Bioconductor release.
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 | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataImport, Sequencing, Software, SomaticMutation, VariantDetection, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | methods, stats, utils, ggplot2, tidyr, rlang, GenomicRanges, IRanges, S4Vectors, VariantAnnotation |
| System Requirements | |
| URL | https://github.com/gbucci/ClonalSim |
| Bug Reports | https://github.com/gbucci/ClonalSim/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClonalSim_1.0.0.tar.gz |
| Windows Binary (x86_64) | ClonalSim_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | ClonalSim_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | ClonalSim_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClonalSim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClonalSim |
| Package Short Url | https://bioconductor.org/packages/ClonalSim/ |
| Package Downloads Report | Download Stats |