# General Linear Mixed Models for Gene-Level Differential Expression

## Documentation for package ‘glmmSeq’ version 0.5.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

fcPlot | Plotly or ggplot fold change plots
ggmodelPlot | Mixed model effects plot using ggplot2
glmmQvals | Glmm Sequencing qvalues
glmmRefit | Refit mixed effects model
glmmRefit.GlmmSeq | Refit mixed effects model
glmmRefit.lmmSeq | Refit mixed effects model
glmmSeq | GLMM with negative binomial distribution for sequencing count data
GlmmSeq-class | An S4 class to define the glmmSeq output
lmmSeq | Linear mixed models for data matrix
lmmSeq-class | An S4 class to define the lmmSeq output
maPlot | MA plots
metadata | Minimal metadata from PEAC
modelPlot | Mixed model effects plot
summary.GlmmSeq | Summarise a 'glmmSeq'/'lmmSeq' object
summary.lmmSeq | Summarise a 'glmmSeq'/'lmmSeq' object
tpm | TPM count data from PEAC