annotatr
Bioc currentAnnotation of Genomic Regions to Genomic Annotations
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30 19 exported
Complexity
6 avg / 25 max
Call network
30 nodes / 29 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
4,930
Files
79
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
11
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.33
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
29.4%
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
20
First release
2017-02-06
Latest release
2026-09-25
Avg cadence
183 days
Cold removal rate
100%
Dep drift
16
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 33includes a package overview page
- Examples that run
- 100%17 run in a plain check
- Exported functions with examples
- 85%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- annotatr HTML
BUGFIXES
- Fix CpG islands read from UCSC database tables (hg38, mm10, mm39, rn6, rn7, danRer10, danRer11, galGal5), and hg19 chromHMM states, which started 1 bp early because UCSC's 0-based starts were used as 1-based. CpG shores, shelves, and inter-CGI regions, built from the islands, are fixed too. Reported, with a fix, by Ryan Yancey (issue #54, PR #55).
From inst/NEWS in the release
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/rcavalcante/annotatr on 2026-10-18.
The R CMD check workflow runs on Linux, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Gm12878_Ezh2_peak_annotations | data.frame | 2,471 × 3 | No other package |
| IDH2mut_v_NBM_multi_data_chr9 | data.frame | 17,682 × 9 | No other package |
| K562_Cjun_peak_annotations | data.frame | 9,847 × 3 | No other package |
| annotations | – | – | – |
Topics
Depended on by (5)
Bioconductor (5)
People
- Raymond G. Cavalcante author maintainer
- Maureen A. Sartor thesis advisor
Cite
Cite this package
Run in R for the authors' entry:
citation("annotatr")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.
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.