R Observatory: Metrics for ChIPexoQual version 1.36.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ChIPexoQual

Bioc current

ChIPexoQual

v1.36.0 · Package record · software · GPL (>=2)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.5 · Apr 25, 2017

Current · Requires R 4.6

1.0 In 19 of 49 releases 3.23

Description

Package with a quality control pipeline for ChIP-exo/nexus data.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

19 10 exported

Complexity

3.2 avg / 20 max

Call network

19 nodes / 13 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

2,143

Files

44

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,145 (53.4%)Tests 211 (9.8%)Docs 546 (25.5%)Vignettes 241 (11.2%)

API

Exported functions

14

Internal functions

9

Recent export changes

v3.6+2 ExoDataBlacklist, formatRegions

v3.5+12 ARCvURCplot, ExoData, ExoDataSubsampling +9 more

Testing

Has tests

Yes

Test-to-code ratio

0.18

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

70%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.4.0

System requirements

–

C++ standard

–

License

GPL (>=2)

License flags

not SPDX, not OSI

History

Versions

19

First release

2017-04-24

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

3

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 · 196 wordsVignettesYes · 1 · dynamicNEWSYes · 0% structuredCitation fileNo

Help pages: 16
Examples that run: 100%14 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Vignette Title HTML

How these are measured

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/welch16/chipexoqual on 2026-10-21.

Docs source (1)

GitHub Pages site last deployed 2018-03-01

How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 2

Name	Class	Size	Also in
blacklists	list	6 elements	3 packages
exoExample	–	–	–

All of ChIPexoQual's data objects

Topics

Software › Technology › Sequencing › ChIPSeq

Software › Technology › Sequencing

Software › AssayDomain › Transcription

Software › WorkflowStep › Visualization

Software › WorkflowStep › QualityControl

Software › BiologicalQuestion › Coverage

Software › WorkflowStep › Alignment

Maintainer: Rene Welch

Available on

CRANr2uBioconductorautoCRANCOPR

People

Rene Welch author maintainer
Dongjun Chung author
Sunduz Keles author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ChIPexoQual")

Format

Welch, R., Chung, D., & Keles, S. (2026). ChIPexoQual: ChIPexoQual (Version 1.36.0) [Computer software]. https://bioconductor.org/packages/ChIPexoQual

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 ChIPexoQual version 1.36.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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