Table 1.

Analysis methods with their associated R packages and details concerning their implementation

Method	R-Package(s)	Multiple DF Test	Library Adjustment Offset	Details
DESeq2	DESeq2 [6]	LRT	DESeq2 size factors	Default settings used, correlation ignored.
DESeq2 ∗	DESeq2 [6]	LRT	DESeq2 size factors	Default settings used, subjects treated as fixed effects to account for correlation.
edgeR	edgeR [4]	LRT	TMM offset	Default settings used, correlation ignored.
edgeR ∗	edgeR [4]	LRT	TMM offset	Default settings used, subjects treated as fixed effects to account for correlation.
limma	limma [9, 23]	Moderated F-test	NA	Count data transformed using the voom function. The duplicateCorrelation function was used with subject id as a blocking factor to account for correlation.
GEE	Custom R Functions, geepack [27]	Wald χ2 Test	DESeq2 size factors	Models fit using exchangeable working correlation structure. For small sample estimators, custom functions were created by modifying code from the geesmv package [28] to make it compatible with geepack and enable the use of offsets.
LMM	lmerTest [29]	F-test	NA	Data transformed using the variance stabilizing transformation from the DESeq2 package.
NBMM-AGQ	GLMMadaptive [30]	LRT	DESeq2 size factors	Model fit using the mixed_model function with a negative binomial distribution. Default settings used for all other parameters.
NBMM-LP	glmmADMB [31]	LRT	DESeq2 size factors	Model fit using the glmmadmb function with a negative binomial distribution. Default settings used for all other parameters.
NBMM-PL	Custom R Function	LRT	DESeq2 size factors	Custom function was created drawing from the glmm.nb function in the NBZIMM package [21]. Function was created to be compatible with the lmerTest package [29] in order for Satterthwaite degrees of freedom to be calculated.
rmRNAseq	rmRNAseq [18]	Moderated F-statistic with bootstrapped p-values	NA	Model fit using the TC_CAR1 function with the default parameters.