R Observatory: Metrics for compcodeR version 1.48.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

compcodeR

Bioc current

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

v1.48.0 · software · GPL (>= 2)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.14 · Apr 14, 2014

Current · Requires R 4.6

1.0 In 25 of 49 releases 3.23

Description

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

103 36 exported

Complexity

7.2 avg / 77 max

Call network

103 nodes / 115 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

15,791

Files

136

Compiled share

0%

Has compiled src

No

Language breakdown

R 7,681 (48.6%)Tests 2,951 (18.7%)Docs 3,095 (19.6%)Vignettes 2,064 (13.1%)

API

Exported functions

36

Internal functions

66

Recent export changes

v3.7−1 SAMseq.createRmd

Testing & CI

Has tests

Yes

Test-to-code ratio

0.38

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

3

Dep constraint coverage

7.1%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0

System requirements

–

C++ standard

–

License

GPL (>= 2)

License flags

SPDX valid, OSI approved

History

Versions

25

First release

2014-04-11

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

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 · 67 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 61%
References docs: 27%

Topics

Software › ResearchField › Immunology › ImmunoOncology

Software › Technology › Sequencing › RNASeq

Software › BiologicalQuestion › DifferentialExpression

People

Charlotte Soneson author maintainer
Paul Bastide author
Mélina Gallopin author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("compcodeR")

Format

Soneson, C., Bastide, P., & Gallopin, M. (2026). compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods (Version 1.48.0) [Computer software]. https://bioconductor.org/packages/compcodeR

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 compcodeR version 1.48.0 [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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