ChIPpeakAnno
Bioc currentBatch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
Release Lineage
Entered 2.5 · Oct 28, 2009
Current · Requires R 4.6
Description
The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
92 55 exported
Complexity
11.6 avg / 76 max
Call network
92 nodes / 74 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
23,130
Files
274
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
56
Internal functions
37
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
57.1%
Unsafe pattern score
0
Dep constraint coverage
13.2%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
34
First release
2010-04-13
Latest release
2026-04-28
Avg cadence
168 days
Cold removal rate
100%
Dep drift
53
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 99%
- Documented parameters
- 84%
- Return-value docs
- 91%
- References docs
- 24%
Topics
Depended on by (13)
People
Jianhong Ou
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ChIPpeakAnno")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.