R Observatory: Metrics for GeDi version 1.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GeDi

Bioc current

Defining and visualizing the distances between different genesets

v1.7.1 · software · MIT + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.19 · May 1, 2024

Current · Requires R 4.6

1.0 In 5 of 49 releases 3.23

Description

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

50 38 exported

Complexity

5.4 avg / 88 max

Call network

50 nodes / 51 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

10,149

Files

144

Compiled share

0%

Has compiled src

No

Language breakdown

R 5,949 (58.6%)Tests 783 (7.7%)Docs 2,234 (22%)Vignettes 1,183 (11.7%)

API

Exported functions

38

Internal functions

11

Recent export changes

v3.22+3 .cluster_markov, .map_to_color, path_to_GeDi −4 calculateJaccard, calculateKappa, calculateSorensenDice 1 more

v3.20+6 goDistance, kMeansClustering, louvainClustering +3 more −1 goSimilarity

Testing & CI

Has tests

Yes

Test-to-code ratio

0.13

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

33.3%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4.0

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

5

First release

2024-06-25

Latest release

2026-04-28

Avg cadence

161 days

Cold removal rate

100%

Dep drift

8

LOC over versions

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

Documentation

READMEYes · 240 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideNo

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

Topics

Software › Infrastructure › GUI

Software › BiologicalQuestion › GeneSetEnrichment

Software

Software › AssayDomain › Transcription

Software › Technology › Sequencing › RNASeq

Software › WorkflowStep › Visualization

Software › StatisticalMethod › Clustering

Software › WorkflowStep › Pathways

Software › WorkflowStep › ReportWriting

Software › WorkflowStep › Pathways › GO

Software › WorkflowStep › Pathways › KEGG

Software › WorkflowStep › Pathways › Reactome

Software › ShinyApps

People

Annekathrin Nedwed author maintainer
Federico Marini author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GeDi")

Format

Nedwed, A., & Marini, F. (2026). GeDi: Defining and visualizing the distances between different genesets (Version 1.7.1) [Computer software]. https://bioconductor.org/packages/GeDi

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 GeDi version 1.7.1 [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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