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GeneTonic

Bioc current

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

v3.6.0 · software · MIT + file LICENSE
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Release Lineage

Entered 3.11 · Apr 28, 2020

Current · Requires R 4.6

1.0 In 13 of 49 releases 3.23

Description

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

62 52 exported

Complexity

4.8 avg / 30 max

Call network

62 nodes / 67 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

17,436

Files

150

Compiled share

0%

Has compiled src

No

Language breakdown

R 10,071 (57.8%)Tests 2,168 (12.4%)Docs 4,236 (24.3%)Vignettes 961 (5.5%)

API

Exported functions

55

Internal functions

10

Testing & CI

Has tests

Yes

Test-to-code ratio

0.22

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

0

Dep constraint coverage

6.7%

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

13

First release

2020-05-06

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

10

LOC over versions

v3.11: 9,631 LOCv3.12: 11,456 LOCv3.13: 14,923 LOCv3.14: 15,885 LOCv3.15: 17,088 LOCv3.16: 17,250 LOCv3.17: 17,422 LOCv3.18: 17,422 LOCv3.19: 17,448 LOCv3.20: 17,392 LOCv3.21: 17,436 LOCv3.22: 17,436 LOCv3.23: 17,436 LOC

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

Documentation

Documentation
READMEYes · 300 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductYesContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
11%

Topics

Software › Infrastructure › GUI
Software › AssayDomain › GeneExpression
Software
Software › AssayDomain › Transcription
Software › ResearchField › Transcriptomics
Software › WorkflowStep › Visualization
Software › BiologicalQuestion › DifferentialExpression
Software › WorkflowStep › Pathways
Software › WorkflowStep › ReportWriting
Software › BiologicalQuestion › GeneSetEnrichment
Software › WorkflowStep › Annotation
Software › WorkflowStep › Pathways › GO
Software › ShinyApps

Depended on by (3)

Bioconductor (3)

carnation GeDi mosdef

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