R Observatory: Metrics for GenomicScores version 2.24.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenomicScores

Bioc current

Infrastructure to work with genomewide position-specific scores

v2.24.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.5 · Apr 25, 2017

Current · Requires R 4.6

1.0 In 19 of 49 releases 3.23

Description

Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

34 5 exported

Complexity

6.2 avg / 21 max

Call network

34 nodes / 23 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

3,364

Files

129

Compiled share

0%

Has compiled src

No

Language breakdown

R 1,848 (54.9%)Tests 1 (0%)Docs 799 (23.8%)Vignettes 716 (21.3%)

API

Exported functions

5

Internal functions

29

Recent export changes

v3.8−1 MafDb

v3.6+2 makeGScoresPackage, MafDb

Testing

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

80%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

16.7%

Unsafe pattern score

0

Dep constraint coverage

21.1%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.5

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

19

First release

2017-09-01

Latest release

2026-04-28

Avg cadence

157 days

Cold removal rate

100%

Dep drift

11

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

READMEYes · 358 wordsVignettesYes · 1 · dynamicNEWSYes · 0% structured · mentions 2.24.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 9 (2 internal)
Examples that run: 71%5 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 67%
Help pages citing references: 67%

Vignettes (1)

An introduction to the GenomicScores package HTML

Changes in 2.24.0 (Bioconductor 3.23)

BUG FIXES

Sanitize AnnotationHub resource filenames in annotation package creation with 'makeGScoresPackage()'.

From NEWS in the release

How these are measured

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/rcastelo/genomicscores on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Coverage (1)

Coverage reporting

How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 33

Name	Class	Size	Also in
AlphaMissense.v2023.hg38.chr20	–	–	–
AlphaMissense.v2023.hg38.chr21	–	–	–
AlphaMissense.v2023.hg38.chr22	–	–	–
GScoresResourcesMetadata	data.frame	35 × 3	No other package
avgs	vector	20 elements	No other package
avgsbmi	vector	19 elements	No other package
cadd.v1.6.hg38.chr20	–	–	–
cadd.v1.6.hg38.chr21	–	–	–
cadd.v1.6.hg38.chr22	–	–	–
gwcgr_chr20-22_151123	–	–	–
metadata_AlphaMissense.v2023.hg19	data.frame	25 × 18	No other package
metadata_AlphaMissense.v2023.hg38	data.frame	25 × 18	No other package
metadata_MCAP.v1.0.hg19	data.frame	24 × 18	No other package
metadata_cadd.v1.6.hg19	data.frame	24 × 18	No other package
metadata_cadd.v1.6.hg38	data.frame	24 × 18	No other package
metadata_fitCons.UCSC.hg19	data.frame	22 × 18	No other package
metadata_linsight.UCSC.hg19	data.frame	23 × 18	No other package
metadata_phastCons100way.UCSC.hg19	data.frame	92 × 18	No other package
metadata_phastCons100way.UCSC.hg38	data.frame	333 × 18	No other package
metadata_phastCons27way.UCSC.dm6	data.frame	151 × 18	No other package
metadata_phastCons30way.UCSC.hg38	data.frame	333 × 18	No other package
metadata_phastCons35way.UCSC.mm39	data.frame	54 × 18	No other package
metadata_phastCons46wayPlacental.UCSC.hg19	data.frame	92 × 18	No other package
metadata_phastCons46wayPrimates.UCSC.hg19	data.frame	92 × 18	No other package
metadata_phastCons60way.UCSC.mm10	data.frame	59 × 18	No other package
metadata_phastCons7way.UCSC.hg38	data.frame	455 × 18	No other package
metadata_phyloP100way.UCSC.hg19	data.frame	92 × 18	No other package
metadata_phyloP100way.UCSC.hg38	data.frame	333 × 18	No other package
metadata_phyloP35way.UCSC.mm39	data.frame	53 × 18	No other package
metadata_phyloP60way.UCSC.mm10	data.frame	59 × 18	No other package
phyloP100way.UCSC.hg38.chr20	–	–	–
phyloP100way.UCSC.hg38.chr21	–	–	–
phyloP100way.UCSC.hg38.chr22	–	–	–

All of GenomicScores's data objects

Topics

Software › Infrastructure

Software › ResearchField › Genetics

Software › WorkflowStep › Annotation

Software › Technology › Sequencing

Software › BiologicalQuestion › Coverage

Software › Technology › AnnotationHubSoftware

Maintainer: Robert Castelo

Available on

CRANr2uBioconductorautoCRANCOPR

Depended on by (33)

Show 31 packagesHide 31 packages

Bioconductor (33)

AlphaMissense.v2023.hg19 AlphaMissense.v2023.hg38 appreci8R ATACseqQC cadd.v1.6.hg19 cadd.v1.6.hg38 fitCons.UCSC.hg19 MafDb.1Kgenomes.phase1.GRCh38 MafDb.1Kgenomes.phase1.hs37d5 MafDb.1Kgenomes.phase3.GRCh38 MafDb.1Kgenomes.phase3.hs37d5 MafDb.ExAC.r1.0.GRCh38 MafDb.ExAC.r1.0.hs37d5 MafDb.ExAC.r1.0.nonTCGA.GRCh38 MafDb.ExAC.r1.0.nonTCGA.hs37d5 MafDb.gnomAD.r2.1.GRCh38 MafDb.gnomAD.r2.1.hs37d5 MafDb.gnomADex.r2.1.GRCh38 MafDb.gnomADex.r2.1.hs37d5 MafDb.TOPMed.freeze5.hg19 MafDb.TOPMed.freeze5.hg38 MafH5.gnomAD.v4.0.GRCh38 phastCons100way.UCSC.hg19 phastCons100way.UCSC.hg38 phastCons30way.UCSC.hg38 phastCons35way.UCSC.mm39 phastCons7way.UCSC.hg38 phyloP35way.UCSC.mm39 primirTSS RareVariantVis +3 more

Suggested by (1)

methrix

People

Robert Castelo author maintainer
Pau Puigdevall contributor
Pablo Rodríguez contributor

Cite

Cite this package

Run in R for the authors' entry:

citation("GenomicScores")

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.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for GenomicScores version 2.24.0 [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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