R Observatory: Metrics for annotatr version 1.38.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

annotatr

Bioc current

Annotation of Genomic Regions to Genomic Annotations

v1.38.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.4 · Oct 18, 2016

Current · Requires R 4.6

1.0 In 20 of 49 releases 3.23

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.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

30 19 exported

Complexity

6.1 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 →

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Lowest coverage

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

Code

Structure

Lines of code

4,930

Files

84

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,434 (49.4%)Tests 800 (16.2%)Docs 1,224 (24.8%)Vignettes 472 (9.6%)

API

Exported functions

20

Internal functions

11

Recent export changes

v3.5+3 build_ah_annots, builtin_annotations, builtin_genomes −2 supported_annotations, supported_genomes

Testing & CI

Has tests

Yes

Test-to-code ratio

0.33

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

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

2026-04-28

Avg cadence

182 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

READMEYes · 11 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › WorkflowStep › Annotation

Software › BiologicalQuestion › GenomeAnnotation

Software › ResearchField › FunctionalGenomics

Software › WorkflowStep › Visualization

Depended on by (7)

Bioconductor (7)

borealis dmrseq epiRomics ramr scmeth SOMNiBUS ExpHunterSuite

People

Raymond G. Cavalcante author maintainer
Maureen A. Sartor ths

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("annotatr")

Format

Cavalcante, R. G., & Sartor, M. A. (2026). annotatr: Annotation of Genomic Regions to Genomic Annotations (Version 1.38.0) [Computer software]. https://bioconductor.org/packages/annotatr

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for annotatr version 1.38.0 [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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