R Observatory: Metrics for glmmSeq version 0.5.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

glmmSeq

0.5.8Package record

General Linear Mixed Models for Gene-Level Differential Expression

0packages depend

4.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Myles LewisCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.5.8

15/10/2026

glmmTMB is now in Suggests rather than Imports. glmmSeq() and

glmmRefit() only require it when method = "glmmTMB".

Fix compatibility with lme4 2.1.0, which no longer finds variables defined

inside the calling function when fitting models. This fix applies to glmmSeq(),

lmmSeq() and glmmRefit().

From NEWS.md in the release

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. 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: 4.9 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
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.8

READMEYes · 140 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.5.8Citation fileNoWebsiteYes · pkgdown

Help pages: 13
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

glmmSeq

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #6,614 · ~13/day · ~406/mo

Releases R versions

Daily download trend is not available in this view yet.

51230 days

1.3K90 days

4.9K1 year

Compare downloads with other packages →

Also on120 r2u47 c2d4u

How downloads are counted

Repository

myles-lewis/glmmseq ↗Account: myles-lewis

26Stars

12Forks

12Open issues

2Open PRs

3Releases

301Commits

9Commit identities

bioinformaticsdifferential-gene-expressiongene-expressiontranscriptomicscranglmmmixed-models

301 commits · Last activity 2026-10-20 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-01 · 232026-08-27 · 26

How these are measured

PracticesBeta

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

Checks run against github.com/myles-lewis/glmmseq on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-20

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing glmmSeq adds 114 packages (57 with compiled code, 103 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 >= 3.6.0

Imports (15)

car emmeansstatsggplot2 ggpubrgraphicsMASSlme4 lmerTest kableExtra mcprogressmethodsplotly qvalue pbapply

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown DESeq2 edgeR glmmTMB

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 (6)

Myles Lewis

Author, Maintainer since 0.5.1 (2022)

Author

Author

Contributor

Contributor · added in 0.5.8

Anna Surace

Contributor

Previously maintained by Katriona Goldmann (0.0.1 to 0.4.0).

Releases (8)

Pick two releases to compare their code metrics.

0.5.8Latest
record
2026-10-20 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-20 12:27 UTC, so it stayed less than the time between readings.
R
R 4.6.0 released · 2026-04-24
0.5.7
record
2025-10-02 · 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
record
2022-10-08 · diff ↗
0.5.1
record
2022-09-12 · diff ↗
0.4.0
record
2022-08-12 · diff ↗ ·
removed 4 exports
glmerApply, glmmGene, lmerApply, pairedPlot

added 2 exports
ggmodelPlot, glmmRefit
unarchivedReturned to CRAN
2022-07-11
0.2.0
record
2022-07-11 · diff ↗ ·
added 2 exports
lmerApply, lmmSeq
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
record
2021-03-30 · diff ↗
0.0.1
record
2021-03-11

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2021-03-11
Total releases: 8 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 39 KB / 1 file
Download size: 1.7 MB

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., Rios Santini, D., Sciacca, E., & Surace, A. (2026). glmmSeq: General Linear Mixed Models for Gene-Level Differential Expression (Version 0.5.8) [Computer software]. https://doi.org/10.32614/CRAN.package.glmmSeq

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 glmmSeq version 0.5.8 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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