R Observatory: Metrics for locuszoomr version 0.3.10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

locuszoomr

0.3.10

Gene Locus Plot with Gene Annotations

0packages depend

8.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Myles LewisFirst published 2023-11-0114 releasesCRAN page ↗GitHub ↗

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.

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.

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

Health

CRAN checks

13OK

Slowest check: 15.6 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

20

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 9 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-28
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 244 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

8.1K

CRAN downloads in the past year

Rank #3,770 · ~22/day · ~674/mo

Releases R versions

Daily download trend is not available in this view yet.

86930 days

2.4K90 days

8.1K1 year

Compare downloads with other packages →

Also on141 r2u735 bioconda

Repository

GitHub ↗ myles-lewis/locuszoomr

61Stars

5Forks

4Open issues

1Open PRs

9Releases

598Commits

4Contributors

License GPL-3.0 · 598 commits · Last activity 2026-07-20 · 0% stars, 30d

Stars over time

2025-07-25 · 462026-07-19 · 61

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/myles-lewis/locuszoomr on 2026-08-16.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (20)

AnnotationFilter BiocGenerics cowplot dplyr ensembldb GenomeInfoDb GenomicRanges gggrid ggplot2 ggrepelgraphicsgrDevicesgridIRanges LDlinkR memoise plotly rlang rtracklayer zoo

LinkingTo (0)

none

Suggests (4)

AnnotationHub EnsDb.Hsapiens.v75 knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Myles Lewis

Author, Maintainer

Authors (1)

Myles Lewis

Author, Maintainer

Package Timeline

14 releases. Pick two to compare their code metrics. R releases are shown for context.

0.3.10Latest
2026-07-19 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.3.8
2025-03-03 · diff ↗
0.3.7
2025-02-10 · diff ↗
0.3.6
2025-01-26 · diff ↗
0.3.5
2024-09-15 · diff ↗
0.3.4
2024-09-06 · diff ↗
0.3.2
2024-08-19 · diff ↗
0.3.1
2024-07-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.0
2024-04-16 · diff ↗
0.2.1
2024-02-17 · diff ↗
0.2.0
2024-01-08 · diff ↗
0.1.3
2023-12-06 · diff ↗
0.1.2
2023-11-02 · diff ↗

Show 2 earlier events

0.1.1
2023-11-01
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-01
Total releases: 14 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 85 KB / 1 file
Download size: 2.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("locuszoomr")

Format

Lewis, M. (2026). locuszoomr: Gene Locus Plot with Gene Annotations (Version 0.3.10) [Computer software]. https://doi.org/10.32614/CRAN.package.locuszoomr

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 locuszoomr version 0.3.10 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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