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. 2020 Jan 17;10:1331. doi: 10.3389/fgene.2019.01331

Table 1.

List of the differential expression analysis methods.

Method Distribution assumption Designed for Test statistic Run time Version [Ref.] Input
BPSC Beta-Poisson Single cell z-test Hours 0.99.2 (Vu et al., 2016) CPM
DEsingle Zero-Inflated Negative Binomial Single cell Likelihood ratio test Hours 1.2.1 (Miao et al., 2018) raw counts
MAST Normal (Generalized linear hurdle) Single cell Likelihood ratio test Minutes 1.8.2 (Finak et al., 2015) log2(CPM+1)
monocle Normal (Generalized additive model) Single cell Likelihood ratio test Minutes 2.10.1(Qiu et al., 2017) raw counts
DESeq2 Negative Binomial Bulk cell Wald test Minutes 1.22.2 (Love et al., 2014) raw counts
edgeR Negative Binomial Bulk cell Quasi-likelihood F-test Minutes 3.24.3 (Robinson et al., 2010) raw counts
limmatrend Normal (linear model) Bulk cell Empirical-Bayes Moderated t-statistics Seconds (Law et al., 2014) log2(CPM+1)
t-test Normal General t-test Seconds (Welch, 1947) log2(CPM+1)
Wilcoxon Nonparametric General Wilcoxon Minutes (Hollander et al., 2013) log2(CPM+1)