R Observatory: Metrics for ChIPQC version 1.48.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ChIPQC

Bioc current

Quality metrics for ChIPseq data

v1.48.3 · Package record · software · GPL (>= 3)

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

Quality metrics for ChIPseq data.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

29 0 exported

Complexity

6.8 avg / 66 max

Call network

29 nodes / 15 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

5,318

Files

68

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,657 (50%)Docs 2,023 (38%)Vignettes 638 (12%)

API

Exported functions

2

Internal functions

29

Testing

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

0%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

28%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5.0

System requirements

–

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

25

First release

2014-07-27

Latest release

2026-05-08

Avg cadence

181 days

Cold removal rate

–

Dep drift

12

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

READMENoVignettesYes · 2 · dynamicNEWSYes · mentions 1.48.3Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 43includes a package overview page
Examples that run: 100%40 run in a plain check
Exported functions with examples: not tracked
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 7%

Vignettes (2)

Changes in 1.48.3 (Bioconductor 3.23)

Add package anchors to \link{...} cross-references that target topics in other packages (GenomicRanges, DiffBind, BiocParallel), eliminating the `Found Rd file(s) with Rd \link{} targets missing package anchors'' R CMD check NOTE. 9 man/*.Rd` files updated. No code change.

From inst/NEWS.Rd in the release

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

Datasets

Bundled datasets · 5

Name	Class	Size	Also in
blacklist.hg19	–	–	–
exampleExp	ChIPQCexperiment	0 elements	10 packages
example_QCexperiment	data.frame	6 × 6	No other package
tamoxifen	ChIPQCexperiment	0 elements	10 packages
tamoxifenQC	data.frame	11 × 11	No other package

All of ChIPQC's data objects

Topics

Software › Technology › Sequencing

Software › Technology › Sequencing › ChIPSeq

Software › WorkflowStep › QualityControl

Software › WorkflowStep › ReportWriting

Maintainer: Tom Carroll

Available on

CRANr2uBioconductorautoCRANCOPR

People (from the free-text Author field)

Cite

Cite this package

Run in R for the authors' entry:

citation("ChIPQC")

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 ChIPQC version 1.48.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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