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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