R Observatory: Metrics for csaw version 1.46.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

csaw

Bioc current

ChIP-Seq Analysis with Windows

v1.46.0 · Package record · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.0 · Oct 14, 2014

Current · Requires R 4.6

1.0 In 24 of 49 releases 3.23

Description

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

127 51 exported

Complexity

3.7 avg / 15 max

Call network

127 nodes / 143 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

12,934

Files

144

Compiled share

14.4%

Has compiled src

Yes

Language breakdown

R 3,530 (27.3%)C/C++/src 1,865 (14.4%)Tests 4,167 (32.2%)Docs 3,321 (25.7%)Vignettes 51 (0.4%)

API

Exported functions

53

Internal functions

34

Recent export changes

v3.8+8 asDGEList, calculateCPM, consolidateOverlaps +5 more −1 consolidateSizes

v3.6+1 scaleControlFilter −2 reformList, checkList

Testing

Has tests

Yes

Test-to-code ratio

1.18

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

12.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

2 externalC++11, GNU make

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

24

First release

2015-03-11

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

17

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 · 48 wordsVignettesYes · 1 · dynamicNEWSYesCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 37
Examples that run: 100%36 run in a plain check (1 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 97%
Help pages citing references: 24%

Vignettes (1)

Introduction HTML

How these are measured

Repository practices

Bioconductor git repository

Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.

No development-tooling practices detected in the Bioconductor git repository.

How this is detected

Topics

Software › WorkflowStep › MultipleComparison

Software › Technology › Sequencing › ChIPSeq

Software › WorkflowStep › Normalization

Software › Technology › Sequencing

Software › BiologicalQuestion › Coverage

Software › ResearchField › Genetics

Software › WorkflowStep › Annotation

Software › BiologicalQuestion › DifferentialPeakCalling

Maintainer: Aaron Lun

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (10)

Show all 13 packagesHide all 13 packages

Bioconductor (8)

csawBook diffHic epigraHMM extraChIPs icetea mutscan NADfinder vulcan

CRAN (2)

hicream treediff

Suggested by (3)

chipseqDB DiffBind GRaNIE

People

Aaron Lun author maintainer
Gordon Smyth author

Cite

Cite this package

Run in R for the authors' entry:

citation("csaw")

The package provides a citation file, so citation() returns the authors' own entry.

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 csaw version 1.46.0 [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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