Package: glmmSeq
Title: General Linear Mixed Models for Gene-Level Differential
        Expression
Version: 0.5.7
Authors@R: 
    c(person(given = "Myles",family = "Lewis",
    role = c("aut", "cre"),
    email = "myles.lewis@qmul.ac.uk",
    comment = c(ORCID = "0000-0001-9365-5345")),
    person(given = "Katriona",family = "Goldmann",
    role = c("aut"),
    email = "k.goldmann@qmul.ac.uk",
    comment = c(ORCID = "0000-0002-9073-6323")),
    person(given = "Elisabetta",family = "Sciacca",
    role = c("aut"),
    email = "e.sciacca@qmul.ac.uk",
    comment = c(ORCID = "0000-0001-7525-1558")),
    person(given = "Cankut",family = "Cubuk",
    role = c("ctb"),
    email = "c.cubuk@qmul.ac.uk",
    comment = c(ORCID = "0000-0003-4646-0849")),
    person(given = "Anna", family = "Surace",
    role = c("ctb"),
    email = "a.surace@qmul.ac.uk",
    comment = c(ORCID = "0000-0001-9589-3005")))
Description: 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>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews:
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Language: en-gb
URL: https://myles-lewis.github.io/glmmSeq/,
        https://github.com/myles-lewis/glmmSeq
BugReports: https://github.com/myles-lewis/glmmSeq/issues
Suggests: knitr, rmarkdown, DESeq2, edgeR
VignetteBuilder: knitr
Depends: R (>= 3.6.0)
Imports: car, emmeans, stats, ggplot2, ggpubr, glmmTMB, graphics, MASS,
        lme4, lmerTest, kableExtra, mcprogress, methods, plotly,
        qvalue, pbapply
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev
Repository: https://myles-lewis.r-universe.dev
Date/Publication: 2025-10-01 19:55:13 UTC
RemoteUrl: https://github.com/myles-lewis/glmmseq
RemoteRef: HEAD
RemoteSha: 8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7
NeedsCompilation: no
Packaged: 2026-07-04 01:42:36 UTC; root
Author: Myles Lewis [aut, cre] (ORCID: <https://orcid.org/0000-0001-9365-5345>),
  Katriona Goldmann [aut] (ORCID:
    <https://orcid.org/0000-0002-9073-6323>),
  Elisabetta Sciacca [aut] (ORCID:
    <https://orcid.org/0000-0001-7525-1558>),
  Cankut Cubuk [ctb] (ORCID: <https://orcid.org/0000-0003-4646-0849>),
  Anna Surace [ctb] (ORCID: <https://orcid.org/0000-0001-9589-3005>)
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>