R Observatory: Metrics for scran version 1.40.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scran

Bioc current

Methods for Single-Cell RNA-Seq Data Analysis

v1.40.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.3 · May 4, 2016

Current · Requires R 4.6

1.0 In 21 of 49 releases 3.23

Description

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

211 53 exported

Complexity

3.5 avg / 15 max

Call network

211 nodes / 172 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

21,598

Files

151

Compiled share

5.6%

Has compiled src

Yes

Language breakdown

R 8,620 (39.9%)C/C++/src 1,201 (5.6%)Tests 6,164 (28.5%)Docs 5,469 (25.3%)Vignettes 144 (0.7%)

API

Exported functions

75

Internal functions

109

Recent export changes

v3.9+2 correlateGenes, denoisePCANumber −1 simpleSumFactors

v3.8+14 cleanSizeFactors, combineMarkers, combinePValues +11 more −2 exploreData, selectorPlot

Testing & CI

Has tests

Yes

Test-to-code ratio

0.72

testthat edition

–

CI present

No

CI type

[]

PR gated

No

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

–

System requirements

1

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

21

First release

2016-08-10

Latest release

2026-04-28

Avg cadence

170 days

Cold removal rate

100%

Dep drift

47

LOC over versions

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

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 28%

Topics

Software › ResearchField › Immunology › ImmunoOncology

Software › WorkflowStep › Normalization

Software › Technology › Sequencing

Software › Technology › Sequencing › RNASeq

Software

Software › AssayDomain › GeneExpression

Software › ResearchField › Transcriptomics

Software › Technology › SingleCell

Software › StatisticalMethod › Clustering

Depended on by (104)

CRAN (2)

mixhvg Canek

People

Aaron Lun author maintainer
Karsten Bach author
Jong Kyoung Kim contributor
Antonio Scialdone contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scran")

Format

Lun, A., Bach, K., Kim, J. K., & Scialdone, A. (2026). scran: Methods for Single-Cell RNA-Seq Data Analysis (Version 1.40.0) [Computer software]. https://bioconductor.org/packages/scran

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 scran version 1.40.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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