R Observatory: Metrics for PureCN version 2.18.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PureCN

Bioc current

Copy number calling and SNV classification using targeted short read sequencing

v2.18.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.3 · May 4, 2016

Current · Requires R 4.6

1.0 In 21 of 49 releases 3.23

Description

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

253 44 exported

Complexity

5 avg / 141 max

Call network

253 nodes / 416 edges

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

Call graph

Open call graph →

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Lowest coverage

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

Code

Structure

Lines of code

17,685

Files

206

Compiled share

0%

Has compiled src

No

Language breakdown

R 9,508 (53.8%)Tests 1,817 (10.3%)Docs 3,346 (18.9%)Vignettes 3,014 (17%)

API

Exported functions

44

Internal functions

207

Recent export changes

v3.9+2 processMultipleSamples, segmentationHclust −1 findBestNormal

v3.8+2 calculateIntervalWeights, filterIntervals −1 plotBestNormal

Testing & CI

Has tests

Yes

Test-to-code ratio

0.19

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

10.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

21

First release

2016-07-01

Latest release

2026-04-28

Avg cadence

186 days

Cold removal rate

100%

Dep drift

20

LOC over versions

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

Documentation

READMEYes · 493 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 98%
Return-value docs: 95%
References docs: 16%

Topics

Software › AssayDomain › CopyNumberVariation

Software

Software › Technology › Sequencing

Software › BiologicalQuestion › VariantAnnotation

Software › BiologicalQuestion › VariantDetection

Software › BiologicalQuestion › Coverage

Software › ResearchField › Immunology › ImmunoOncology

People

Markus Riester author maintainer
Angad P. Singh author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PureCN")

Format

Riester, M., & Singh, A. P. (2026). PureCN: Copy number calling and SNV classification using targeted short read sequencing (Version 2.18.0) [Computer software]. https://bioconductor.org/packages/PureCN

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

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

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for PureCN version 2.18.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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