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glmmSeq v0.5.5

  • Improve error handling if all genes give errors

glmmSeq v0.5.4

  • 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


glmmSeq v0.5.1

CRAN release: 2022-09-12

  • 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

CRAN release: 2022-08-12


glmmSeq v0.3.0

  • 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

  • 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

  • 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

CRAN release: 2022-07-11

  • Add lmmSeq function for gaussian linear mixed models

glmmSeq v0.1.2

  • Fix CMD check errors

glmmSeq v0.1.1

Bug Fixes
  • Fix colours in pairedPlots and modelPlots

glmmSeq v0.1.0

CRAN release: 2021-03-30

  • 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

CRAN release: 2021-03-11

  • This is the initial build of glmmSeq