ChIPseeker
Bioc currentChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Release Lineage
Entered 2.14 · Apr 14, 2014
Current · Requires R 4.6
Description
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
114 34 exported
Complexity
6.1 avg / 50 max
Call network
114 nodes / 140 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
11,268
Files
121
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
40
Internal functions
80
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
39
Dep constraint coverage
3.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2014-08-14
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
100%
Dep drift
33
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 66 (2 internal)includes a package overview page
- Examples that run
- 29%2 run in a plain check · 4 never run · 1 hold no code
- Exported functions with examples
- 15%
- Documented parameters
- 100%
- Return-value docs
- 87%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/yulab-smu/chipseeker on 2026-10-11.
GitHub Pages site last deployed 2018-03-14
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| gsminfo | data.frame | 103,398 × 14 | 2 packages |
| processedGSM | vector | 1,973,025 elements | 2 packages |
| sample_peaks | data.frame | 150 × 9 | 2 packages |
| tagMatrixList | list | 5 elements | No other package |
| ucsc_release | data.frame | 112 × 4 | 2 packages |
Topics
Depended on by (10)
Show all 14 packagesHide all 14 packages
Bioconductor (10)
Suggested by (4)
People
- Guangchuang Yu author maintainer
- Chun-Hui Gao contributor
- Michael Kluge contributor
- Ming Li contributor
- Hervé Pagès contributor
- Thomas Schwarzl contributor
- Qianwen Wang contributor
- Zhougeng Xu contributor
- Yun Yan contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("ChIPseeker")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1002/cpz1.585, 10.1093/bioinformatics/btv145.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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.