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chipenrich

Bioc current

Gene Set Enrichment For ChIP-seq Peak Data

v2.36.0 · software · GPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.13 · Oct 15, 2013

Current · Requires R 4.6

1.0 In 26 of 49 releases 3.23

Description

ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

79 21 exported

Complexity

3.4 avg / 20 max

Call network

79 nodes / 149 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

8,744

Files

110

Compiled share

0%

Has compiled src

No

Language breakdown

R 5,354 (61.2%)Tests 788 (9%)Docs 2,175 (24.9%)Vignettes 427 (4.9%)

API

Exported functions

21

Internal functions

58

Recent export changes

v3.7+1 peaks2genes
v3.6+1 hybridenrich

Testing & CI

Has tests

Yes

Test-to-code ratio

0.15

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

3.8%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.4.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

26

First release

2013-10-14

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

19

LOC over versions

v2.13: 2,461 LOCv2.14: 2,461 LOCv3.0: 3,340 LOCv3.1: 3,346 LOCv3.2: 3,526 LOCv3.3: 3,519 LOCv3.4: 3,718 LOCv3.5: 6,319 LOCv3.6: 7,250 LOCv3.7: 7,986 LOCv3.8: 7,986 LOCv3.9: 7,986 LOCv3.10: 8,672 LOCv3.11: 8,672 LOCv3.12: 8,672 LOCv3.13: 8,744 LOCv3.14: 8,743 LOCv3.15: 8,743 LOCv3.16: 8,743 LOCv3.17: 8,743 LOCv3.18: 8,743 LOCv3.19: 8,743 LOCv3.20: 8,743 LOCv3.21: 8,744 LOCv3.22: 8,744 LOCv3.23: 8,744 LOC

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

Documentation

Documentation
READMEYes · 48 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
0%

Topics

Software › ResearchField › Immunology › ImmunoOncology
Software › Technology › Sequencing › ChIPSeq
Software › ResearchField › Epigenetics
Software › ResearchField › FunctionalGenomics
Software › BiologicalQuestion › GeneSetEnrichment
Software › BiologicalQuestion › HistoneModification
Software › StatisticalMethod › Regression

People

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("chipenrich")
Wang, K., Cavalcante, R. G., Lee, C., Lee, C., Sartor, M. A., Scott, L. J., & Welch, R. P. (2026). chipenrich: Gene Set Enrichment For ChIP-seq Peak Data (Version 2.36.0) [Computer software]. https://bioconductor.org/packages/chipenrich

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.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for chipenrich version 2.36.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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