R Observatory: Metrics for AnnotationHubData version 1.42.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AnnotationHubData

Bioc current

Transform public data resources into Bioconductor Data Structures

v1.42.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.12 · Apr 4, 2013

Current · Requires R 4.6

1.0 In 27 of 49 releases 3.23

Description

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

164 30 exported

Complexity

2.4 avg / 17 max

Call network

164 nodes / 147 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

7,062

Files

69

Compiled share

0%

Has compiled src

No

Language breakdown

R 5,567 (78.8%)Tests 1 (0%)Docs 1,458 (20.6%)Vignettes 36 (0.5%)

API

Exported functions

45

Internal functions

123

Recent export changes

v3.9+1 validDispatchClass

v3.8+5 getSpeciesList, validSpecies, suggestSpecies +2 more

Testing

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

13.3%

Unsafe pattern score

0

Dep constraint coverage

18.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.2.2

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

27

First release

2013-04-03

Latest release

2026-04-28

Avg cadence

185 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

In the Bioconductor 3.23 release

READMENoVignettesYes · 1 · staticNEWSYes · 33% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12includes a package overview page
Examples that run: 40%4 run in a plain check · 6 never run
Exported functions with examples: 91%
Documented parameters: 99%
Return-value docs: 91%
Help pages citing references: 0%

Vignettes (1)

Introduction to AnnotationHubData HTML

How these are measured

Repository practices

Bioconductor git repository

Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.

1 practice detected in the Bioconductor git repository

Continuous integration (1)

AppVeyor

How this is detected

Datasets

Bundled datasets · 6

Name	Class	Size	Also in
ahm	–	–	–
allTracks	list	144 elements	No other package
annotation_haemcode	data.frame	315 × 9	No other package
badTracks	list	144 elements	No other package
genomeTrackTable	list	144 elements	No other package
haemCodeFileList	data.frame	314 × 1	No other package

All of AnnotationHubData's data objects

Topics

Software › Infrastructure › DataImport

Maintainer: Bioconductor Package Maintainer

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (5)

Bioconductor (5)

AHEnsDbs AHMassBank EuPathDB ExperimentHubData ProteomicsAnnotationHubData

Suggested by (7)

EPICv2manifest GenomicState homosapienDEE2CellScore HubPub humanHippocampus2024 smokingMouse TENET.AnnotationHub

People

Bioconductor Package Maintainer maintainer
Sonali Arora contributor
Marc Carlson contributor
Martin Morgan contributor
Paul Shannon contributor
Lori Shepherd contributor
Dan Tenenbaum contributor

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AnnotationHubData")

Format

Bioconductor Package Maintainer, Arora, S., Carlson, M., Morgan, M., Shannon, P., Shepherd, L., & Tenenbaum, D. (2026). AnnotationHubData: Transform public data resources into Bioconductor Data Structures (Version 1.42.0) [Computer software]. https://bioconductor.org/packages/AnnotationHubData

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 AnnotationHubData version 1.42.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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