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 | |
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/ | |
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/ | |
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 |