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News

glmmSeq v0.5.5

29/09/2022

• Improve error handling if all genes give errors

glmmSeq v0.5.4

25/09/2022

• Add option for likelihood ratio test (LRT) in glmmSeq() and lmmSeq()
• Enable changing of model formula, family and control parameters when refitting model for a single gene in glmmRefit()

glmmSeq v0.5.2

19/09/2022

• Fix passing of ... in parallelisation on windows in glmmSeq() & lmmSeq()

glmmSeq v0.5.1

02/09/2022

• Add option to glmmSeq() to use glmmTMB package for fitting negative binomial GLMM (or other GLM family) models
• Add plab argument to modelPlots to customise p-value labels
• Add mean expression column meanExp to results in @stats$res slot

glmmSeq v0.4.0

10/08/2022

• Further speed enhancements to lmmSeq() using lme4::modular code. Speed increase of around 25%.

glmmSeq v0.3.0

05/08/2022

• Significant update including output of standard error on fitted coefficients for both glmmSeq and lmmSeq
• Add summary function for glmmSeq and lmmSeq to display results for an individual gene
• Reorganised @stats slot in output objects to include more information including DF
• Added option of using Saiterthwaite’s DF method with ANOVA type III tables as option for lmmSeq using the lmerTest package
• Added lmmRefit function to fit an identical (g)lmer model. This can then be passed to the emmeans package for visualisation of more complex models.
• Separated modelPlots (base graphics) and ggmodelPlots (ggplot2)
• Streamlined modelPlots to allow for simplest case gene ~ Time + (1 | ID)

glmmSeq v0.2.2

16/07/2022

• Fast version of lmmSeq(). Improves speed of calculation of type 2 Wald test. Overall speed increase of 25-50%.
• Faster version of glmmSeq()
• Automatically detects id column name from the RE term in the formula

glmmSeq v0.2.1

11/07/2022

• Add ... option to fcPlot which is passed to plotly() or ggplot()
• set annotationPosition=FALSE in fcPlot so arrows/connectors are not moved

glmmSeq v0.2.0

09/07/2022

• Add lmmSeq function for gaussian linear mixed models

glmmSeq v0.1.2

08/07/2022

• Fix CMD check errors

glmmSeq v0.1.1

18/04/2021

Bug Fixes

• Fix colours in pairedPlots and modelPlots

glmmSeq v0.1.0

16/03/2021

Features

• Add progress bars to glmmSeq functions
• Add option returnList to return glmmSeq output as list (to make error catching easier)

Bug Fixes

• Fix missing plots in vignette

glmmSeq v0.0.1

05/03/2021

• This is the initial build of glmmSeq

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.