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OncoSimulR

Bioc current

Forward Genetic Simulation of Cancer Progression with Epistasis

v4.14.0 · Package record · software · GPL (>= 3)
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.0 · Oct 14, 2014

Current · Requires R 4.6

1.0 In 24 of 49 releases 3.23

Description

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

1585 28 exported

Complexity

7.8 avg / 117 max

Call network

1585 nodes / 2921 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

132,502

Files

257

Compiled share

51%

Has compiled src

Yes

Language breakdown

R 7,989 (6%)C/C++/src 67,524 (51%)Tests 32,874 (24.8%)Docs 5,030 (3.8%)Vignettes 19,085 (14.4%)

API

Exported functions

28

Internal functions

127

Recent export changes

v3.5+5 sampledGenotypes, POM, LOD +2 more

Testing

Has tests

Yes

Test-to-code ratio

4.11

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

2

Dep constraint coverage

6.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5.0

System requirements

–

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

24

First release

2014-10-13

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

–

Dep drift

13

LOC over versions

v3.0: 3,986 LOCv3.1: 3,986 LOCv3.2: 19,994 LOCv3.3: 27,406 LOCv3.4: 46,045 LOCv3.5: 52,473 LOCv3.6: 53,850 LOCv3.7: 57,951 LOCv3.8: 57,967 LOCv3.9: 58,029 LOCv3.10: 71,389 LOCv3.11: 72,566 LOCv3.12: 72,567 LOCv3.13: 115,548 LOCv3.14: 115,571 LOCv3.15: 115,571 LOCv3.16: 126,252 LOCv3.17: 126,593 LOCv3.18: 126,608 LOCv3.19: 126,608 LOCv3.20: 126,668 LOCv3.21: 126,669 LOCv3.22: 126,691 LOCv3.23: 132,502 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

In the Bioconductor 3.23 release
READMENoVignettesYes · 1 · dynamicNEWSYes · 67% structuredCitation fileYes · cites a publicationWebsiteYes
Help pages
24
Examples that run
96%23 run in a plain check · 1 never run
Exported functions with examples
100%
Documented parameters
90%
Return-value docs
100%
Help pages citing references
33%
Vignettes (1)
How these are measured

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/rdiaz02/oncosimul on 2026-10-22.

Continuous integration (2)
Travis CI (config file)AppVeyor
Docs source (1)

GitHub Pages site last deployed 2025-06-09

Coverage (1)
Coverage reporting (Codecov)
Git structural (1)
.gitattributes
How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 23
NameClassSizeAlso in
atex2boncosimul22 elementsNo other package
atex4oncosimul24 elementsNo other package
atex5oncosimul24 elementsNo other package
benchmark_1data.frame16 × 39No other package
benchmark_1_0.05data.frame16 × 39No other package
benchmark_2data.frame14 × 38No other package
benchmark_3data.frame14 × 38No other package
ex_missing_drivers_b11oncosimul19 elementsNo other package
ex_missing_drivers_b12oncosimul19 elementsNo other package
examplePosetslist13 elementsNo other package
examplesFitnessEffectslist22 elementsNo other package
mcfLsoncosimul21 elementsNo other package
osioncosimul22 elementsNo other package
osi_with_intsoncosimul23 elementsNo other package
s_3_aoncosimul22 elementsNo other package
s_3_boncosimul22 elementsNo other package
simT2oncosimul22 elementsNo other package
simT3oncosimul22 elementsNo other package
simul_period_1oncosimul22 elementsNo other package
smyelo3v57oncosimul22 elementsNo other package
uvex2oncosimul23 elementsNo other package
uvex3oncosimul22 elementsNo other package
woAntibSoncosimul23 elementsNo other package

All of OncoSimulR's data objects

Topics

Software › BiologicalQuestion
Software › BiologicalQuestion › SomaticMutation
Maintainer
Ramon Diaz-Uriarte

Available on

CRANr2uBioconductorautoCRANCOPR

People

Cite

Cite this package

Run in R for the authors' entry:

citation("OncoSimulR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btx077, 10.1371/journal.pcbi.1007246, 10.1093/bioinformatics/btx663, 10.1186/s12859-015-0466-7.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for OncoSimulR version 4.14.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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