Package: glmmSeq 0.5.6

glmmSeq: General Linear Mixed Models for Gene-Level Differential Expression

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>.

Authors:Myles Lewis [aut, cre], Katriona Goldmann [aut], Elisabetta Sciacca [aut], Cankut Cubuk [ctb], Anna Surace [ctb]

glmmSeq_0.5.6.tar.gz
glmmSeq_0.5.6.zip(r-4.5)glmmSeq_0.5.6.zip(r-4.4)glmmSeq_0.5.6.zip(r-4.3)
glmmSeq_0.5.6.tgz(r-4.5-any)glmmSeq_0.5.6.tgz(r-4.4-any)glmmSeq_0.5.6.tgz(r-4.3-any)
glmmSeq_0.5.6.tar.gz(r-4.5-noble)glmmSeq_0.5.6.tar.gz(r-4.4-noble)
glmmSeq_0.5.6.tgz(r-4.4-emscripten)glmmSeq_0.5.6.tgz(r-4.3-emscripten)
glmmSeq.pdf |glmmSeq.html
glmmSeq/json (API)
NEWS

# Install 'glmmSeq' in R:
install.packages('glmmSeq', repos = c('https://myles-lewis.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/myles-lewis/glmmseq/issues

Pkgdown site:https://myles-lewis.github.io

Datasets:
  • metadata - Minimal metadata from PEAC
  • tpm - TPM count data from PEAC

On CRAN:

Conda:

bioinformaticsdifferential-gene-expressiongene-expressionglmmmixed-modelstranscriptomics

6.13 score 20 stars 45 scripts 322 downloads 8 exports 112 dependencies

Last updated 2 months agofrom:81fcf2cde2. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 18 2025
R-4.5-winNOTEMar 18 2025
R-4.5-macNOTEMar 18 2025
R-4.5-linuxNOTEMar 18 2025
R-4.4-winOKMar 18 2025
R-4.4-macOKMar 18 2025
R-4.4-linuxOKMar 18 2025
R-4.3-winOKMar 18 2025
R-4.3-macOKMar 18 2025

Exports:fcPlotggmodelPlotglmmQvalsglmmRefitglmmSeqlmmSeqmaPlotmodelPlot

Dependencies:abindaskpassbackportsbase64encbootbroombslibcachemcarcarDataclicolorspacecorrplotcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeFormulafsgenericsggplot2ggpubrggrepelggsciggsignifglmmTMBgluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmerTestmagrittrMASSMatrixMatrixModelsmcprogressmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbapplypbkrtestpillarpkgconfigplotlyplyrpolynompromisespurrrquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2rlangrmarkdownrstatixsassscalesSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexTMButf8vctrsviridisLitewithrxfunyaml

glmmSeq

Rendered fromglmmSeq.rmdusingknitr::rmarkdownon Mar 18 2025.

Last update: 2022-10-07
Started: 2020-08-17