ClonalSim
Bioc currentSimulation of Tumor Clonal Evolution with Realistic Sequencing Noise
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 16 exported
Complexity
3.7 avg / 20 max
Call network
18 nodes / 5 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
3,247
Files
42
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
2
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.36
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.6.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22 (1 internal)includes a package overview page
- Examples that run
- 100%21 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 5%
Repository practices
Checks run against github.com/gbucci/clonalsim on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Topics
People
- Gabriele Bucci author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ClonalSim")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.