Suggests: knitr, rmarkdown, kableExtra, edgeR
methods, plotly, qvalue, pbapply, pbmcapply

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>.
Suggests: knitr, rmarkdown, kableExtra, DESeq2, edgeR, emmeans
Imports: MASS, car, stats, ggplot2, ggpubr, graphics, lme4, lmerTest,

Imports: MASS, car, stats, ggplot2, ggpubr, glmmTMB, graphics, lme4,
lmerTest, methods, plotly, qvalue, pbapply, pbmcapply

Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
Imports: methods, TMB (>= 1.7.6), lme4 (>= 1.1-10), Matrix, nlme
Suggests: knitr, testthat, MASS, lattice, ggplot2, mlmRev, bbmle, pscl,
Packaged: 2017-02-19 19:15:52 UTC; molliebrooks1

Suggests: knitr, testthat, MASS, lattice, ggplot2, mlmRev, bbmle (>=
Packaged: 2017-10-25 20:52:44 UTC; molliebrooks1

Packaged: 2017-12-08 15:19:51 UTC; molliebrooks

Suggests: knitr, rmarkdown, testthat, MASS, lattice, ggplot2, mlmRev,
bbmle (>= 1.0.19), pscl, MCMCpack, coda, reshape2
Packaged: 2018-05-10 09:32:50 UTC; molliebrooks