Package: ClonalSim 1.0.0

Gabriele Bucci

ClonalSim: Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

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.

Authors:Gabriele Bucci [aut, cre]

ClonalSim_1.0.0.tar.gz
ClonalSim_1.0.0.zip(r-4.7)ClonalSim_1.0.0.zip(r-4.6)ClonalSim_1.0.0.zip(r-4.5)
ClonalSim_1.0.0.tgz(r-4.6-any)ClonalSim_1.0.0.tgz(r-4.5-any)
ClonalSim_1.0.0.tar.gz(r-4.7-any)ClonalSim_1.0.0.tar.gz(r-4.6-any)
ClonalSim_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ClonalSim/json (API)
NEWS

# Install 'ClonalSim' in R:
install.packages('ClonalSim', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gbucci/clonalsim/issues

On BioConductor:ClonalSim-1.1.0(bioc 3.24)ClonalSim-1.0.0(bioc 3.23)

softwaresequencingsomaticmutationvariantdetectioncoveragevisualizationdataimport

4.65 score 1 stars 170 downloads 19 exports 88 dependencies

Last updated from:fb76c2bd93 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE216
linux-devel-x86_64OK394
source / vignettesOK286
linux-release-x86_64OK395
macos-release-arm64OK221
macos-oldrel-arm64OK195
windows-develOK329
windows-releaseOK360
windows-oldrelOK316
wasm-releaseOK162

Exports:applyBiologicalNoiseClonalSimDatagetClonalStructuregetMetadatagetMutationsgetObservedVAFgetSimParamsgetTrueVAFplotshowsimulateDepthsimulateSequencingReadssimulateTumorsummarytoDataFrametoGRangestoPyClonetoSciClonetoVCF

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml

Introduction to ClonalSim

Gabriele Bucci

Rendered fromIntroduction_to_ClonalSim.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-21
Started: 2025-10-29