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Table 1 Software tools for identifying DE genes using scRNAseq data

From: Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tool Prog. Language Input format Model Year/ version URL
SCDE R Read counts Poisson and negative binomial model 2014/2.2.0 http://bioconductor.org/packages/release/bioc/html/scde.html
MAST R TPM/FPKM Generalized linear model 2015/1.0.5 http://bioconductor.org/packages/release/bioc/html/MAST.html
scDD R TPM/FPKM Conjugate Dirichlet process mixture 2016/0.99.0 http://bioconductor.org/packages/devel/bioc/html/scDD.html
EMDomics R TPM/FPKM Non-parametric earth mover’s distance 2016/2.4.0 https://www.bioconductor.org/packages/release/bioc/html/EMDomics.html
D3E Python Read counts Cramér-von Mises test, Kolmogorov-Smirnov test, likelihood ratio test 2016/ https://github.com/hemberg-lab/D3E
Monocle2 R TPM/FPKM Generalized additive model 2014/2.2.0 http://bioconductor.org/packages/release/bioc/html/monocle.html
SINCERA R TPM/FPKM/Read counts Welch’s t-test and Wilcoxon rank sum test 2015/ https://research.cchmc.org/pbge/sincera.html
edgeR R Read counts Negative binomial model, Exact test 2010/3.16.5 http://bioconductor.org/packages/release/bioc/html/edgeR.html
DESeq2 R Read counts Negative binomial model, Exact test 2014/1.14.1 http://bioconductor.org/packages/release/bioc/html/DESeq2.html
DEsingle R Read counts Zero inflated negative binomial 2018/1.2.0 https://bioconductor.org/packages/release/bioc/html/DEsingle.html
SigEMD R TPM/FPKM Non-parametric earth mover’s distance 2018/0.21.1 https://github.com/NabaviLab/SigEMD