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 · 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.

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 →

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Lowest coverage

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

Code

Structure

Lines of code

6,499

Files

53

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 & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

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

READMEYes · 50 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 50%
References docs: 0%

Topics

Software › ResearchField › Genetics

Software › Infrastructure

Software › Technology › Sequencing

Software › WorkflowStep › Annotation

Software › BiologicalQuestion › Coverage

Software › BiologicalQuestion › GenomeAnnotation

Depended on by (1037)

CRAN (51)

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 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 SummarizedExperiment version 1.42.0 [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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