R Observatory: Metrics for GALLO version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GALLO

2.0Package record

Genomic Annotation in Livestock for Positional Candidate LOci

0packages depend

9.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Pablo FonsecaCRAN page ↗GitHub ↗

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.

Changes in 2.0

The GALLO v2.0 introduces new tools for pleiotropic effect detection, estimation of effective marker numbers and independent chromosomal segments, gene-level p-value calculation, and network-based visualization and gene prioritization. This is the most substantial update since GALLO’s initial release. These additions expand users’ ability to integrate high-throughput data, uncover hidden patterns across datasets, mine previously reported associations, and more efficiently investigate the genetic architecture of complex traits in livestock.

From NEWS in the release

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. 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: 5.8 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0

READMEYes · 633 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 2.0Citation fileYes · cites a publication

Help pages: 43 (27 internal)
Examples that run: 82%9 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 44%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 16%

Vignettes (1)

Genomic Annotation in Livestock for positional candidate LOci: GALLO HTML

How these are measured

Downloads

9.5K

CRAN downloads in the past year

Rank #5,365 · ~26/day · ~794/mo

Releases R versions

Daily download trend is not available in this view yet.

61030 days

1.5K90 days

9.5K1 year

Compare downloads with other packages →

Also on101 r2u

How downloads are counted

Repository

pablobio/gallo ↗Account: pablobio

14Stars

0Forks

0Open issues

0Open PRs

0Releases

125Commits

1Commit identities

License file reads as GPL-3.0 · 125 commits · Last activity 2021-02-26 · 0% stars, 30d · The default branch showed an older version (1.1) than CRAN on 2026-10-18

Responsiveness

not measured

Stars over time

2025-05-22 · 122026-07-07 · 14

How these are measured

PracticesBeta

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

Checks run against github.com/pablobio/gallo on 2026-10-18.

Docs source (1)

GitHub Pages site last deployed 2020-07-09

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing GALLO adds 77 packages (37 with compiled code, 74 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Pablo Fonseca

Author, Maintainer since 0.99.0 (2020)

Angela Cánovas

Author

Gabriele Marras

Author

Aroa Suarez-Vega

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0Latest
record
2026-02-10 · current release · diff ↗ ·
added 2 exports
Gene_PPA, Net_embedding
R
R 4.5.0 released · 2025-04-11
1.5
record
2024-06-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4
record
2024-03-13 · diff ↗ ·
added 6 exports
NetCen, NetVis, Nmarkers_SimpleM, Nseg_chr, PleioChiTest, gene_pval
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.3
record
2021-11-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2
record
2021-04-08 · diff ↗
1.1
record
2020-11-06 · diff ↗
1.0
record
2020-10-08 · diff ↗
0.99.0
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("GALLO")

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

It points to 10.1093/gigascience/giaa149.

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 v2026-10-22. 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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