Name | Statistical testing | Normalization approach | Target application areas |
---|---|---|---|
edgeR [12] | Negative Binomial Model, Conditional Maximum Likelihood to estimate parameters, Exact Test | TMM, UQN | SAGE [1], MPSS [29], PMAGE [30], miRAGE [31] and SACO [32] among others |
DESeq [6] | Negative Binomial Model, local regression to estimate parameters, Exact Test | Normalization by median | |
baySeq [15] | Negative Binomial Model, empirical Bayes to estimate parameters | RPM, TMM | |
NOISeq [16] | Non-parametric approach | RPM, RPKM, UQN | |
Cuffdiff [14] | t-test | RPM, RPKM, UQN | RNA-seq [3] |
Metastats [11] | Non-parametric t-test, Fisher’s Exact Test for small counts | RPM | Metagenomics |