R Observatory: Metrics for GALLO version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GALLO

2.0

Genomic Annotation in Livestock for Positional Candidate LOci

0packages depend

10.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Pablo FonsecaFirst published 2020-09-018 releasesCRAN page ↗

The accurate annotation of genes and Quantitative Trait Loci (QTLs) located within candidate markers and/or regions (haplotypes, windows, CNVs, etc) is a crucial step the most common genomic analyses performed in livestock, such as Genome-Wide Association Studies or transcriptomics. The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an intuitive and straightforward environment to annotate positional candidate genes and QTLs from high-throughput genetic studies in livestock. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chicken, among others.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-gallo

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: 5.8 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

23

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

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
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 633 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 100%
Return-value docs: 100%
References docs: 16%

Downloads

10.4K

CRAN downloads in the past year

Rank #4,291 · ~28/day · ~867/mo

Releases R versions

Daily download trend is not available in this view yet.

32430 days

1.9K90 days

10.4K1 year

Compare downloads with other packages →

Also on150 r2u

Repository

GitHub ↗ pablobio/gallo

14Stars

0Forks

0Open issues

0Open PRs

0Releases

125Commits

1Contributors

License GPL-3.0 · 125 commits · Last activity 2021-02-26 · 0% stars, 30d

Stars over time

2025-05-22 · 122026-07-07 · 14

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/pablobio/gallo on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (23)

circlize data.table doParallel dplyr ggplot2graphicsgrDevicesforeachlatticeparallelRColorBrewer rtracklayerstatsstringr unbalhaarutilsDT webshot igraph visNetwork CompQuadFormMatrixreticulate

LinkingTo (0)

none

Suggests (4)

Hmisc knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Pablo Fonseca

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0Latest
2026-02-10 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.5
2024-06-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4
2024-03-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.3
2021-11-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2
2021-04-08 · diff ↗
1.1
2020-11-06 · diff ↗
1.0
2020-10-08 · diff ↗
0.99.0
2020-09-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-01
Total releases: 8 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.2 MB / 4 files
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GALLO")

Format

Fonseca, P., Cánovas, A., Marras, G., & Suarez-Vega, A. (2026). GALLO: Genomic Annotation in Livestock for Positional Candidate LOci (Version 2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.GALLO

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 GALLO version 2.0 [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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