R Observatory: Metrics for SummarizedExperiment version 1.42.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SummarizedExperiment

Bioc current

A container (S4 class) for matrix-like assays

v1.42.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.2 · Oct 14, 2015

Current · Requires R 4.6

1.0 In 22 of 49 releases 3.23

Description

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

53 9 exported

Complexity

4.1 avg / 20 max

Call network

53 nodes / 41 edges

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

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

6,499

Files

51

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,934 (45.1%)Tests 2 (0%)Docs 2,007 (30.9%)Vignettes 1,556 (23.9%)

API

Exported functions

21

Internal functions

38

Recent export changes

v3.7+1 makeSummarizedExperimentFromLoom −2 saveHDF5SummarizedExperiment, loadHDF5SummarizedExperiment

v3.5+3 .DollarNames.RangedSummarizedExperiment, saveHDF5SummarizedExperiment, loadHDF5SummarizedExperiment −1 rowRanges

Testing

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

90.5%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

50%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

22

First release

2015-12-31

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

100%

Dep drift

9

LOC over versions

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

Documentation

In the Bioconductor 3.23 release

READMEYes · 50 wordsVignettesYes · 2 · dynamicNEWSYes · 33% structured · mentions 1.42.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 50%
Help pages citing references: 0%

Vignettes (2)

Changes in 1.42.0 (Bioconductor 3.23)

No significant changes in this version.

From NEWS in the release

How these are measured

Repository practices

Upstream repositoryBeta

Checks run against github.com/bioconductor/summarizedexperiment on 2026-10-25.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v4 (2026-10-20)

Topics

Software › ResearchField › Genetics

Software › Infrastructure

Software › Technology › Sequencing

Software › WorkflowStep › Annotation

Software › BiologicalQuestion › Coverage

Software › BiologicalQuestion › GenomeAnnotation

Maintainer: Hervé Pagès

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (925)

Show 85 packagesHide 85 packages

People

Hervé Pagès author maintainer
Jim Hester author
Martin Morgan author
Valerie Obenchain author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SummarizedExperiment")

Format

Pagès, H., Hester, J., Morgan, M., & Obenchain, V. (2026). SummarizedExperiment: A container (S4 class) for matrix-like assays (Version 1.42.0) [Computer software]. https://bioconductor.org/packages/SummarizedExperiment

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 SummarizedExperiment version 1.42.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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