epiSeeker
Bioc currentepiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
This package implements functions to analyze multi-omics epigenetic data. Data of fragment type and base type are supported by epiSeeker. It provides functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statistical methods to estimate the significance of overlap among peak data sets, and motif analysis. It incorporates the GEO database for users to compare their own dataset with those deposited in the 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, overlap of peaks or genes, and the single-base resolution epigenetic data by considering the strand, motif, and additional information.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
142 34 exported
Complexity
5.2 avg / 35 max
Call network
142 nodes / 146 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
13,614
Files
165
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
41
Internal functions
108
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
57
Dep constraint coverage
3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.6.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 84 (2 internal)includes a package overview page
- Examples that run
- 100%47 run in a plain check (2 of them under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- epiSeeker.html HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/yulab-smu/episeeker on 2026-10-25.
GitHub Pages site last deployed 2026-10-10
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| demo_bisseq | data.frame | 50 × 4 | No other package |
| demo_bmdata | – | – | – |
| demo_peak | – | – | – |
| gsminfo | data.frame | 103,398 × 14 | 2 packages |
| peakAnno | – | – | – |
| peakAnnoList | list | 5 elements | No other package |
| processedGSM | vector | 1,973,025 elements | 2 packages |
| pwm_obj | – | – | – |
| sample_peaks | data.frame | 150 × 9 | 2 packages |
| seq2gene_result | vector | 193 elements | No other package |
| tagMatrix | matrix | 664 × 500 | No other package |
| ucsc_release | data.frame | 112 × 4 | 2 packages |
Topics
People
- Guangchuang Yu author maintainer funder
- 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("epiSeeker")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 v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.