… Multiple methods are used interchangeably for this purpose in the literature. Yet, there are …
of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample …

… datasets, results heavily depend on the applied DA method. Moreover, the preprocessing
of microbiome sequencing count data strongly influence results … (Figs 37 and 38 in S1 File), …

… methods for zero estimation, with promising results [38, 60]. Furthermore, DESeq and
edgeR-trimmed mean by M values (TMM) make … normalization techniques to several datasets from …

… The Wrench [38] normalization corrects the compositional … methods on 106 experiment
datasets with binary outcomes … the significant taxa between methods across the 106 datasets (Fig. …

… model can also be fit using the R package GLMMadaptive [38] … from a large reference
microbiome dataset (non-parametric … To produce an overall score, we first convert the total FDR …

… In a large cardiometabolic disease dataset, we showcase … healthy adults [33, 37, 38] before
signal implantation, using study … 23, 30], our results suggest DA methods borrowed from RNA-…

… distinguish the terms microbiome and microbiota and … The combination of results from both
approaches with the … The number of counts in a HTS dataset reflect the proportion of counts …

… a key technique for the analysis of the human microbiome, its … method is optimal for all
types of metagenomics datasets. … shown to have a substantial impact on the analysis [38, 46] …

… and to reproduce results obtained from experimental data. … differential abundance tests
using 38 experimental datasets … data for validating differential abundance methods while strictly …

… multiple methods for differential abundance analysis in this section including edgeR [38], …
especially in the case of a shuffled microbiome dataset where correlations are actually zero. …