R Observatory: Metrics for locuszoomr version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

locuszoomr

1.2.0Package record

Gene Locus Plot with Gene Annotations

0packages depend

11.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Myles LewisCRAN page ↗GitHub ↗Issues ↗

Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' https://my.locuszoom.org, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API https://ldlink.nih.gov/?tab=apiaccess to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots doi:10.1093/bioadv/vbaf006.

Changes in 1.2.0

26/09/2026

Added Get eQTL button to zoom() to pull LDlink API eQTL information and

overlay this on GWAS data.

Added overlay_plotly() and eqtl_plotly().

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("locuszoomr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("myles-lewis/locuszoomr")

Development version from myles-lewis/locuszoomr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-locuszoomr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 13.8 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 9 earlier changesHide 9 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-06-04
ERROR12 OK, 1 ERROR2026-05-28
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-16
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMEYes · 307 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.2.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 26
Examples that run: 100%11 run in a plain check
Exported functions with examples: 48%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

11.1K

CRAN downloads in the past year

Rank #2,830 · ~30/day · ~922/mo

Releases R versions

Daily download trend is not available in this view yet.

2.6K30 days

5.1K90 days

11.1K1 year

Compare downloads with other packages →

Also on151 r2u808 bioconda

How downloads are counted

Repository

myles-lewis/locuszoomr ↗Account: myles-lewis

65Stars

5Forks

4Open issues

1Open PRs

11Releases

722Commits

4Commit identities

License file reads as GPL-3.0 · 722 commits · Last activity 2026-10-09 · +3.2% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-25 · 502026-10-13 · 65

How these are measured

PracticesBeta

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

Checks run against github.com/myles-lewis/locuszoomr on 2026-10-18.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Installing locuszoomr adds 73 packages (39 with compiled code, 70 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 7 more not on CRAN are not measured.

Depends (1)

R >= 3.5

Imports (21)

AnnotationFilter BiocGenerics cowplot ensembldb GenomeInfoDb GenomicRanges gggrid ggplot2graphicsgrDevicesgridgtools htmltools IRanges LDlinkR memoise plotly Rcpp rlang rtracklayer shiny

LinkingTo (1)

Rcpp

Suggests (13)

AnnotationDbi AnnotationHub dplyr DT EnsDb.Hsapiens.v75 ggrepel knitr org.Hs.eg.db rmarkdown shinycssloaders shinyFeedback shinyWidgets zoo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Myles Lewis

Author, Maintainer since 0.1.1 (2023)

Tom Willis

Contributor · added in 1.0.0

Releases (17)

Pick two releases to compare their code metrics.

1.2.0Latest
record
2026-10-09 · current release · diff ↗
1.1.0
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2026-09-17 · diff ↗ ·
added 1 export
sanity_check
1.0.0
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2026-09-03 · diff ↗ ·
added 1 export
zoom
0.3.10
record
2026-07-19 · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.3.8
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2025-03-03 · diff ↗
0.3.7
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2025-02-10 · diff ↗
0.3.6
record
2025-01-26 · diff ↗
0.3.5
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2024-09-15 · diff ↗
0.3.4
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2024-09-06 · diff ↗
0.3.2
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2024-08-19 · diff ↗
0.3.1
record
2024-07-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.0
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2024-04-16 · diff ↗
0.2.1
record
2024-02-17 · diff ↗

Show 5 earlier eventsHide 5 earlier events

0.2.0
record
2024-01-08 · diff ↗ ·
added 3 exports
genetracks_grob, link_recomb, quick_peak
0.1.3
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2023-12-06 · diff ↗
0.1.2
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2023-11-02 · diff ↗
0.1.1
record
2023-11-01
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-01
Total releases: 17 / 3 yrs
License: GPL (>= 3) OSI · relicensed from Artistic-2.0 in 0.2.0
Minimum R: ≥ 3.5
Bundled data: 85 KB / 1 file
Download size: 6.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("locuszoomr")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioadv/vbaf006.

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 locuszoomr version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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