R Observatory: Metrics for tidybulk version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tidybulk

Bioc current

Brings transcriptomics to the tidyverse

v2.2.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.11 · Apr 28, 2020

Current · Requires R 4.6

1.0 In 13 of 49 releases 3.23

Description

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

156 6 exported

Complexity

4.6 avg / 41 max

Call network

156 nodes / 196 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

19,416

Files

172

Compiled share

0%

Has compiled src

No

Language breakdown

R 11,458 (59%)Tests 2,632 (13.6%)Docs 3,293 (17%)Vignettes 2,033 (10.5%)

API

Exported functions

31

Internal functions

141

Recent export changes

v3.22+4 get_X_cibersort, scale_x_log10_reverse, scale_y_log10_reverse +1 more −26 %>%, arrange, as_tibble 23 more

v3.20+1 resolve_complete_confounders_of_non_interest

Testing & CI

Has tests

Yes

Test-to-code ratio

0.23

testthat edition

–

CI present

Yes

CI type

["github-actions","travis"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

9.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

13

First release

2020-06-08

Latest release

2026-04-28

Avg cadence

168 days

Cold removal rate

100%

Dep drift

15

LOC over versions

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

Documentation

READMEYes · 1,679 wordsVignettesYes · dynamicpkgdown siteYesNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 99%
Return-value docs: 100%
References docs: 67%

Topics

Software › AssayDomain

Software › Infrastructure

Software › Technology › Sequencing › RNASeq

Software › BiologicalQuestion › DifferentialExpression

Software › AssayDomain › GeneExpression

Software › WorkflowStep › Normalization

Software › StatisticalMethod › Clustering

Software › WorkflowStep › QualityControl

Software › Technology › Sequencing

Software › AssayDomain › Transcription

Software › ResearchField › Transcriptomics

Depended on by (3)

Bioconductor (3)

tidyexposomics tidyomics cellNexus

People

Stefano Mangiola author maintainer
Maria Doyle contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tidybulk")

Format

Mangiola, S., & Doyle, M. (2026). tidybulk: Brings transcriptomics to the tidyverse (Version 2.2.0) [Computer software]. https://bioconductor.org/packages/tidybulk

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 tidybulk version 2.2.0 [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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