R Observatory: Metrics for bamsignals version 1.44.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bamsignals

Bioc current

Extract read count signals from bam files

v1.44.1 · software · GPL-2

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.1 · Apr 17, 2015

Current · Requires R 4.6

1.0 In 23 of 49 releases 3.23

Description

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

43 0 exported

Complexity

2.1 avg / 7 max

Call network

43 nodes / 26 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

2,198

Files

30

Compiled share

30.4%

Has compiled src

Yes

Language breakdown

R 349 (15.9%)C/C++/src 669 (30.4%)Tests 472 (21.5%)Docs 343 (15.6%)Vignettes 365 (16.6%)

API

Exported functions

4

Internal functions

11

Testing & CI

Has tests

Yes

Test-to-code ratio

1.35

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

20%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5.0

System requirements

1

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

23

First release

2015-04-16

Latest release

2026-05-21

Avg cadence

183 days

Cold removal rate

–

Dep drift

1

LOC over versions

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

Documentation

READMEYes · 47 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: 100%
References docs: 0%

Topics

Software › Infrastructure › DataImport

Software › Technology › Sequencing

Software › BiologicalQuestion › Coverage

Software › WorkflowStep › Alignment

Depended on by (8)

Bioconductor (8)

crupR fourSynergy karyoploteR normr segmenter AneuFinder chromstaR Genefusiondiscover

People

Alessandro Mammana author maintainer
Johannes Helmuth author

At a glance

Version: 1.44.1
Category: software
License: GPL-2
Requires R: ≥ 4.6
Maintainer: Johannes Helmuth
Entered: 3.1 · Apr 17, 2015
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.5.0)

Imports

methodsBiocGenericsBiocRcpp (>= 0.10.6)IRangesBiocGenomicRangesBioc

Suggests

testthat (>= 0.9)RsamtoolsBiocBiocStyleBiocknitr rmarkdown

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bamsignals")

Format

Mammana, A., & Helmuth, J. (2026). bamsignals: Extract read count signals from bam files (Version 1.44.1) [Computer software]. https://bioconductor.org/packages/bamsignals

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 bamsignals version 1.44.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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