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

From: Experimental design and quantitative analysis of microbial community multiomics

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