R Observatory: Metrics for pcaExplorer version 3.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pcaExplorer

Bioc current

Interactive Visualization of RNA-seq Data Using a Principal Components Approach

v3.6.0 · software · MIT + file LICENSE

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 provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

21 17 exported

Complexity

10.4 avg / 121 max

Call network

21 nodes / 12 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

6,363

Files

91

Compiled share

0%

Has compiled src

No

Language breakdown

R 4,180 (65.7%)Tests 205 (3.2%)Docs 1,024 (16.1%)Vignettes 954 (15%)

API

Exported functions

17

Internal functions

4

Testing & CI

Has tests

Yes

Test-to-code ratio

0.05

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

50%

Unsafe pattern score

42

Dep constraint coverage

9.1%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

21

First release

2016-05-15

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

12

LOC over versions

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

Documentation

READMEYes · 641 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › Immunology › ImmunoOncology

Software › WorkflowStep › Visualization

Software › Technology › Sequencing › RNASeq

Software › StatisticalMethod › DimensionReduction

Software › StatisticalMethod › PrincipalComponent

Software › WorkflowStep › QualityControl

Software › Infrastructure › GUI

Software › WorkflowStep › ReportWriting

Software › ShinyApps

Depended on by (1)

Bioconductor (1)

DASC

People

Federico Marini author maintainer

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pcaExplorer")

Format

Marini, F. (2026). pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach (Version 3.6.0) [Computer software]. https://bioconductor.org/packages/pcaExplorer

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 pcaExplorer version 3.6.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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