Introduction | Key Features | Installation | Basic Usage | Simple Simulation | Accessing Results | Visualization | Understanding the Noise Model | Biological Noise: Beta Distribution | Technical Sequencing Noise | Depth Overdispersion | Binomial Read Sampling | Common Use Cases | Low Purity Tumor | High Coverage Sequencing | Low Coverage Sequencing | Ideal Data (No Noise) | Including Germline Variants | Bioconductor Integration | Export to GRanges | Export to VCF | Export for Other Tools | PyClone Format | SciClone Format | Simple CSV | Benchmarking Workflow | Advanced: Custom Clonal Structures | Complex Hierarchies | Accessing Clonal Structure | Session Information | References
Package: ClonalSim 1.1.0
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:
ClonalSim_1.1.0.tar.gz
ClonalSim_1.1.0.zip(r-4.7)ClonalSim_1.1.0.zip(r-4.6)ClonalSim_1.1.0.zip(r-4.5)
ClonalSim_1.1.0.tgz(r-4.6-any)ClonalSim_1.1.0.tgz(r-4.5-any)
ClonalSim_1.1.0.tar.gz(r-4.7-any)ClonalSim_1.1.0.tar.gz(r-4.6-any)
ClonalSim_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClonalSim/json (API)
| # Install 'ClonalSim' in R: |
| install.packages('ClonalSim', repos = c('https://bioc.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
Last updated from:6048f4bf99. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 246 | ||
| linux-devel-x86_64 | OK | 466 | ||
| source / vignettes | OK | 294 | ||
| linux-release-x86_64 | OK | 483 | ||
| macos-release-arm64 | OK | 242 | ||
| macos-oldrel-arm64 | OK | 230 | ||
| windows-devel | OK | 323 | ||
| windows-release | OK | 263 | ||
| windows-oldrel | OK | 313 | ||
| wasm-release | OK | 158 |
Exports:applyBiologicalNoiseClonalSimDatagetClonalStructuregetMetadatagetMutationsgetObservedVAFgetSimParamsgetTrueVAFplotshowsimulateDepthsimulateSequencingReadssimulateTumorsummarytoDataFrametoGRangestoPyClonetoSciClonetoVCF
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml
