R Observatory: Metrics for scMultiome version 1.12.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scMultiome

Bioc current

Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets

v1.12.0 · experiment · CC BY-SA 4.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.17 · Apr 26, 2023

Current · Requires R 4.6

1.0 In 7 of 49 releases 3.23

Description

Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

28 18 exported

Complexity

3.6 avg / 42 max

Call network

28 nodes / 15 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

5,335

Files

82

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,744 (32.7%)Tests 272 (5.1%)Docs 3,052 (57.2%)Vignettes 267 (5%)

API

Exported functions

19

Internal functions

10

Recent export changes

v3.20+3 AR_drug, PBMC_10x, TEADi_resistance

v3.19+1 tfMotifs

Testing & CI

Has tests

Yes

Test-to-code ratio

0.16

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

0%

Unsafe pattern score

3

Dep constraint coverage

7.7%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

CC BY-SA 4.0

License flags

not SPDX, not OSI

History

Versions

7

First release

2023-09-26

Latest release

2026-04-28

Avg cadence

175 days

Cold removal rate

–

Dep drift

2

LOC over versions

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

Documentation

READMEYes · 444 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 67%
Return-value docs: 100%
References docs: 47%

Topics

ExperimentData › PackageTypeData

ExperimentData › PackageTypeData › ExperimentHub

ExperimentData › TechnologyData › SequencingData › SingleCellData

ExperimentData › AssayDomainData › ExpressionData

ExperimentData › TechnologyData › SequencingData

ExperimentData › OrganismData › Homo_sapiens_Data

ExperimentData › SpecimenSource › CellCulture

ExperimentData › SpecimenSource › Tissue

ExperimentData › RepositoryData › GEO

Depended on by (2)

Bioconductor (2)

epiregulon epiregulon.extra

People

Xiaosai Yao maintainer author
Aleksander Chlebowski author
Aaron Lun author
Tomasz Włodarczyk author
Shiqi Xie contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scMultiome")

Format

Yao, X., Chlebowski, A., Lun, A., Włodarczyk, T., & Xie, S. (2026). scMultiome: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets (Version 1.12.0) [Computer software]. https://bioconductor.org/packages/scMultiome

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 scMultiome version 1.12.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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