R Observatory: Metrics for glmmSeq version 0.5.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

glmmSeq

0.5.7

General Linear Mixed Models for Gene-Level Differential Expression

0packages depend

5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Myles LewisFirst published 2021-03-117 releasesCRAN page ↗GitHub ↗

Using mixed effects models to analyse longitudinal gene expression can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, and are less optimal for analysing longitudinal data. This package provides negative binomial and Gaussian mixed effects models to fit gene expression and other biological data across repeated samples. This is particularly useful for investigating changes in RNA-Sequencing gene expression between groups of individuals over time, as described in: Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M. J., & Pitzalis, C. (2022) Nature medicine doi:10.1038/s41591-022-01789-0.

Install

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

install.packages("glmmSeq", 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/glmmSeq")

Development version from myles-lewis/glmmSeq. 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-glmmseq

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: 4.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

16

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 140 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

5K

CRAN downloads in the past year

Rank #6,670 · ~14/day · ~421/mo

Releases R versions

Daily download trend is not available in this view yet.

32930 days

1.2K90 days

5K1 year

Compare downloads with other packages →

Also on151 r2u15 c2d4u

Repository

GitHub ↗ myles-lewis/glmmseq

25Stars

11Forks

12Open issues

2Open PRs

3Releases

290Commits

8Contributors

bioinformaticsdifferential-gene-expressiongene-expressiontranscriptomicscranglmmmixed-models

290 commits · Last activity 2025-10-01 · 0% stars, 30d

Stars over time

2025-06-22 · 222026-07-07 · 25

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/myles-lewis/glmmseq on 2026-08-23.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (16)

car emmeansstatsggplot2 ggpubr glmmTMBgraphicsMASSlme4 lmerTest kableExtra mcprogressmethodsplotly qvalue pbapply

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown DESeq2 edgeR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Myles Lewis

Author, Maintainer

Authors (3)

Myles Lewis

Author, Maintainer

Katriona Goldmann

Author

Elisabetta Sciacca

Author

Contributors (2)

Cankut Cubuk

Contributor

Anna Surace

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.5.7Latest
2025-10-02 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.5.5
2022-10-08 · diff ↗
0.5.1
2022-09-12 · diff ↗
0.4.0
2022-08-12 · diff ↗
0.2.0
2022-07-11 · diff ↗
unarchivedReturned to CRAN
2022-07-11
archivedRemoved from CRAN
2022-05-22
check issues were not corrected in time Does not use 'edgeR' conditionally, and it was uninstallable recently
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1.0
2021-03-30 · diff ↗
0.0.1
2021-03-11
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-11
Total releases: 7 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 39 KB / 1 file
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("glmmSeq")

Format

Lewis, M., Cubuk, C., Goldmann, K., Sciacca, E., & Surace, A. (2025). glmmSeq: General Linear Mixed Models for Gene-Level Differential Expression (Version 0.5.7) [Computer software]. https://doi.org/10.32614/CRAN.package.glmmSeq

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 glmmSeq version 0.5.7 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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