R Observatory: Metrics for Biostrings version 2.80.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Biostrings

Bioc current

Efficient manipulation of biological strings

v2.80.2 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 1.4 · May 17, 2004

Current · Requires R 4.6

1.0 In 45 of 49 releases 3.23

Description

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

661 65 exported

Complexity

3.8 avg / 39 max

Call network

661 nodes / 848 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

38,238

Files

222

Compiled share

30.8%

Has compiled src

Yes

Language breakdown

R 12,075 (31.6%)C/C++/src 11,765 (30.8%)Tests 3,565 (9.3%)Docs 9,243 (24.2%)Vignettes 1,590 (4.2%)

API

Exported functions

167

Internal functions

225

Recent export changes

v3.9+5 xscodes, extract_character_from_XString_by_positions, extract_character_from_XString_by_ranges +2 more

v3.8+1 replaceAmbiguities

Testing

Has tests

Yes

Test-to-code ratio

0.30

testthat edition

–

Docs

Roxygen coverage

98.8%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

44.4%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

45

First release

2004-08-23

Latest release

2026-08-31

Avg cadence

182 days

Cold removal rate

99.3%

Dep drift

21

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 · 47 wordsVignettesYes · 5 · dynamicNEWSYes · 33% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 54 (1 internal)
Examples that run: 96%50 run in a plain check · 2 hold no code
Exported functions with examples: 96%
Documented parameters: 84%
Return-value docs: 66%
Help pages citing references: 19%

Vignettes (5)

How these are measured

Repository practices

Upstream repositoryBeta

Checks run against github.com/bioconductor/biostrings on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Datasets

Bundled datasets · 16

Name	Class	Size	Also in
BLOSUM100	moved_to_pwalign_pkg	24 × 24	2 packages
BLOSUM45	moved_to_pwalign_pkg	25 × 25	2 packages
BLOSUM50	moved_to_pwalign_pkg	24 × 24	3 packages
BLOSUM62	moved_to_pwalign_pkg	25 × 25	3 packages
BLOSUM80	moved_to_pwalign_pkg	25 × 25	2 packages
HNF4alpha	–	–	–
PAM120	moved_to_pwalign_pkg	24 × 24	2 packages
PAM250	moved_to_pwalign_pkg	24 × 24	2 packages
PAM30	moved_to_pwalign_pkg	25 × 25	2 packages
PAM40	moved_to_pwalign_pkg	24 × 24	2 packages
PAM70	moved_to_pwalign_pkg	25 × 25	2 packages
Phylip	–	–	–
hg18chr8_gap	data.frame	9 × 9	No other package
hg18chrY_gap	data.frame	13 × 9	No other package
s_1_sequence	data.frame	1,023 × 1	No other package
yeastSEQCHR1	vector	1 element	No other package

All of Biostrings's data objects

Topics

Software › BiologicalQuestion › SequenceMatching

Software › WorkflowStep › Alignment

Software › Technology › Sequencing

Software › ResearchField › Genetics

Software › Infrastructure › DataImport

Software › Infrastructure › DataRepresentation

Software › Infrastructure

Maintainer: Hervé Pagès

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (618)

Show 90 packagesHide 90 packages

People

Hervé Pagès author maintainer
Patrick Aboyoun author
Vince Carey contributor
Saikat DebRoy author
Nicolas Delhomme contributor
Felix Ernst contributor
Robert Gentleman author
Wolfgang Huber contributor
'matchprobes' vignette
Beryl Kanali contributor
Converted 'MultipleAlignments' vignette from Sweave to RMarkdown
Haleema Khan contributor
Converted 'matchprobes' vignette from Sweave to RMarkdown
Aidan Lakshman contributor
Kieran O'Neill contributor
Valerie Obenchain contributor
Marcel Ramos contributor
Albert Vill contributor
Jen Wokaty contributor
Converted 'matchprobes' vignette from Sweave to RMarkdown
Erik Wright contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Biostrings")

Format

Pagès, H., Aboyoun, P., Carey, V., DebRoy, S., Delhomme, N., Ernst, F., Gentleman, R., Huber, W., Kanali, B., Khan, H., Lakshman, A., O'Neill, K., Obenchain, V., Ramos, M., Vill, A., Wokaty, J., & Wright, E. (2026). Biostrings: Efficient manipulation of biological strings (Version 2.80.2) [Computer software]. https://bioconductor.org/packages/Biostrings

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 Biostrings version 2.80.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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