R Observatory: Metrics for DEGreport version 1.48.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DEGreport

Bioc current

Report of DEG analysis

v1.48.0 · Package record · software · MIT + file LICENSE

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

Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

94 27 exported

Complexity

3.1 avg / 21 max

Call network

94 nodes / 69 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

6,380

Files

311

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,943 (61.8%)Tests 242 (3.8%)Docs 1,844 (28.9%)Vignettes 351 (5.5%)

API

Exported functions

32

Internal functions

64

Recent export changes

v3.8+4 as.DEGSet, degColors, degMA +1 more −2 DEGSetFromDESeq2, DEGSetFromEdgeR

v3.7+2 degSignature, geom_cor

Testing

Has tests

Yes

Test-to-code ratio

0.06

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

24

First release

2014-10-13

Latest release

2026-04-28

Avg cadence

185 days

Cold removal rate

100%

Dep drift

52

LOC over versions

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 · 71 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structuredCitation fileNoWebsiteYes · pkgdown

Help pages: 34includes a package overview page
Examples that run: 100%28 run in a plain check
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 83%
Help pages citing references: 12%

Vignettes (1)

QC and downstream analysis for differential expression RNA-seq HTML

How these are measured

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/lpantano/degreport on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

Docs source (2)

pkgdown

GitHub Pages site last deployed 2025-10-11

Lint, format, editor (1)

RStudio project

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

Datasets

Bundled datasets · 2

Name	Class	Size	Also in
geneInfo	data.frame	49 × 2	No other package
humanGender	–	–	–

All of DEGreport's data objects

Topics

Software › BiologicalQuestion › DifferentialExpression

Software › WorkflowStep › Visualization

Software › Technology › Sequencing › RNASeq

Software › WorkflowStep › ReportWriting

Software › AssayDomain › GeneExpression

Software › ResearchField › Immunology › ImmunoOncology

Maintainer: Lorena Pantano

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (1)

Bioconductor (1)

isomiRs

Suggested by (1)

carnation

People

Lorena Pantano author maintainer
Victor Barrera contributor
Kenneth Daily contributor
John Hutchinson contributor
Radhika Khetani contributor
Rory Kirchner contributor
Thanneer Malai Perumal contributor
Mary Piper contributor
Michael Steinbaugh contributor
Ivo Zeller contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DEGreport")

Format

Pantano, L., Barrera, V., Daily, K., Hutchinson, J., Khetani, R., Kirchner, R., Malai Perumal, T., Piper, M., Steinbaugh, M., & Zeller, I. (2026). DEGreport: Report of DEG analysis (Version 1.48.0) [Computer software]. https://bioconductor.org/packages/DEGreport

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 DEGreport version 1.48.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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