Experimental design and quantitative analysis of microbial community multiomics

Table 3 Tools for feature-wise differential abundance analysis in microbial community taxonomic profiles

Tool	Counts or relative abundance	Normalization	Data transformation	Statistical model	Multivariable association	Random effects	P value calculation	Reference(s)
Metastats	Relative abundance	TSS	None	Nonparametric	No	No	Nonparametric t	[81]
LEfSe	Relative abundance	TSS	None	Nonparametric	No	No	Kruskal-Wallis	[80]
edgeR	Counts	TMM	None	Negative binomial	Yes	No	Fisher’s exact test	[76]
DESeq2	Counts	RLE	None	Negative binomial	Yes	No	Wald’s test	[77]
metagenomeSeq	Counts	CSS	Log	Zero-inflated Gaussian	Yes	No	Moderated t statistic	[74]
limma-voom	Counts	TMM	Voom	Gaussian	Yes	Yes	Moderated t statistic	[78]
MaAsLin	Relative abundance	TSS	Arcsine square root	Gaussian	Yes	Yes	Wald’s test	[75, 138]
ANCOM	Counts	Log ratio	None	Nonparametric	No	No	Mann-Whitney U	[82]
NBMM	Counts	None	None	Negative binomial	Yes	Yes	Wald’s test	[86]
ZINBMM	Counts	None	None	Zero-inflated negative binomial	Yes	Yes	Wald’s test	[103]
ZIBR	Relative abundance	TSS	No	Zero-inflated beta	Yes	Yes	Likelihood ratio	[85]

CSS cumulative sum scaling, RLE relative log expression, TMM trimmed mean by M-value, TSS total-sum scaling

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