R Observatory: Metrics for metaGE version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metaGE

1.2.2Package record

Meta-Analysis for Detecting Genotype x Environment Associations

0packages depend

3.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Annaïg De WalscheCRAN page ↗

Provides functions to perform all steps of genome-wide association meta-analysis for studying Genotype x Environment interactions, from collecting the data to the manhattan plot. The procedure accounts for the potential correlation between studies. In addition to the Fixed and Random models, one can investigate the relationship between QTL effects and some qualitative or quantitative covariate via the test of contrast and the meta-regression, respectively. The methodology is available from: (De Walsche, A., et al. (2025) \doi{10.1371/journal.pgen.1011553}).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("metaGE", 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-metage

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-metaGE

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-metaGE

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 28 (1 internal)includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

metaGE-vignette HTML

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #8,661 · ~10/day · ~306/mo

Releases R versions

Daily download trend is not available in this view yet.

40830 days

1.1K90 days

3.7K1 year

Compare downloads with other packages →

Also on120 r2u4 autocran62 c2d4u

How downloads are counted

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing metaGE adds 64 packages (35 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.0.2

Imports (21)

corrplot data.table dplyr emdbook furrr future ggplot2 ggrepel gplotsgraphicsgrDevicesks purrr qqman Rfaststatsstringr tibble tidyrutilsviridis

LinkingTo (0)

none

Suggests (4)

DT knitr rmarkdown tidyverse

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)

Annaïg De Walsche

Author, Maintainer since 1.0.0 (2023)

Tristan Mary-Huard

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-07-21
1.2.2Latest
record
2025-07-21 · current release · diff ↗
archivedRemoved from CRAN
2025-07-10
requires archived package 'yarrr'
R
R 4.5.0 released · 2025-04-11
1.2.1
record
2025-02-23 · diff ↗
1.2.0
record
2025-02-19 · diff ↗
1.1.0
record
2024-07-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.3
record
2023-09-28 · diff ↗
1.0.2
record
2023-09-11 · diff ↗
1.0.1
record
2023-08-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.0
record
2023-03-08
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-08
Total releases: 8 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.2
Bundled data: 4.2 MB / 2 files
Download size: 4.5 MB

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metaGE")

Format

De Walsche, A., & Mary-Huard, T. (2025). metaGE: Meta-Analysis for Detecting Genotype x Environment Associations (Version 1.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.metaGE

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 metaGE version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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