R Observatory: Metrics for OAtools version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OAtools

Bioc current

Analysis of OpenArray PCR Data

v1.0.0 · Package record · software · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.23 · Apr 29, 2026

Current · Requires R 4.6

1.0 In 1 of 49 releases 3.23

Description

Provides a suite of R functions to analyze gene expression experiments on the OpenArray real-time PCR platform. OAtools fits logistic regressions to fluorescence curves to distinguish between real amplification and false positives. OAtools supports data import, analysis, and visualization through plots and a dynamic HTML report.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

30 10 exported

Complexity

1.1 avg / 3 max

Call network

30 nodes / 28 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.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

2,963

Files

69

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,445 (48.8%)Tests 430 (14.5%)Docs 668 (22.5%)Vignettes 420 (14.2%)

API

Exported functions

10

Internal functions

20

Recent export changes

v3.23+10 buildApp, computeModels, determinePCRResults +7 more

Testing

Has tests

Yes

Test-to-code ratio

0.30

testthat edition

3

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

100%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.6

System requirements

–

C++ standard

–

License

GPL (>= 3)

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

In the Bioconductor 3.23 release

READMEYes · 317 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Analyzing OpenArray Gene Expression Data with OAtools HTML

How these are measured

Repository practices

Upstream repositoryBeta

Checks run against github.com/uwvirology-ngs/oatools on 2026-10-22.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 1

Name	Class	Size	Also in
example_se	–	–	–

All of OAtools's data objects

Topics

Software › Technology › qPCR

Software › AssayDomain › GeneExpression

Software › Infrastructure › DataImport

Software › StatisticalMethod › Regression

Maintainer: Aidan Shea

Available on

CRANr2uBioconductorautoCRANCOPR

People

Aidan Shea author maintainer

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OAtools")

Format

Shea, A. (2026). OAtools: Analysis of OpenArray PCR Data (Version 1.0.0) [Computer software]. https://bioconductor.org/packages/OAtools

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for OAtools version 1.0.0 [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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