R Observatory: Metrics for GenomicAlignments version 1.48.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenomicAlignments

Bioc current

Representation and manipulation of short genomic alignments

v1.48.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.14 · Apr 14, 2014

Current · Requires R 4.6

1.0 In 25 of 49 releases 3.23

Description

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

177 45 exported

Complexity

3.1 avg / 16 max

Call network

177 nodes / 137 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.

Code

Structure

Lines of code

14,807

Files

74

Compiled share

3.7%

Has compiled src

Yes

Language breakdown

R 5,786 (39.1%)C/C++/src 552 (3.7%)Tests 2 (0%)Docs 6,036 (40.8%)Vignettes 2,431 (16.4%)

API

Exported functions

80

Internal functions

114

Recent export changes

v3.5+1 encodingHalves −1 findMateAlignment2

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

33.3%

Unsafe pattern score

0

Dep constraint coverage

40%

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

25

First release

2014-08-21

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

8

LOC over versions

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

Documentation

READMEYes · 41 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 79%
Return-value docs: 72%
References docs: 29%

Topics

Software › Infrastructure

Software › Infrastructure › DataImport

Software › ResearchField › Genetics

Software › Technology › Sequencing

Software › Technology › Sequencing › RNASeq

Software › AssayDomain › SNP

Software › BiologicalQuestion › Coverage

Software › WorkflowStep › Alignment

Software › ResearchField › Immunology › ImmunoOncology

Depended on by (181)

CRAN (6)

PACVr VALERIE alakazam iimi futurize seqmagick

People

Hervé Pagès author maintainer
Halimat C. Atanda contributor
Fedor Bezrukov contributor
Robert Castelo contributor
Martin Morgan author
Valerie Obenchain author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GenomicAlignments")

Format

Pagès, H., Atanda, H. C., Bezrukov, F., Castelo, R., Morgan, M., & Obenchain, V. (2026). GenomicAlignments: Representation and manipulation of short genomic alignments (Version 1.48.0) [Computer software]. https://bioconductor.org/packages/GenomicAlignments

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 GenomicAlignments version 1.48.0 [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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