Tool (package version) | Pipelines | Reference | Citationsa |
---|---|---|---|
edgeR (3.14.0) | (1) Exact test based on NB distribution, (2) GLM with NB family, (3) QL, (4–7) robust GLM with four different prior DF | [32] | 5406 |
DESeq (1.24.0) | (1) Default, exact test based on NB distribution | [45] | 4655 |
DESeq2(1.12.4) | Fits GLM with NB family. (1) Default, (2) independent filtering disabled (setting1), (3) independent filtering disabled and outlier-detection off (setting2) | [10] | 1364 |
limma (3.25.21) | Fits linear models on log-transformed counts. (1) Voom, (2) voom (robust), (3) trended, (4) trended (robust), (5) voom+QW, (6) limmaVST, (7) limmaQN | [33] | 1828 |
NOISeq (2.12.1) | (1) Default, data-adaptive and non-parametric method | [53] | 524 |
baySeq (2.6.0) | (1) Default, Bayesian methods with empirical prior distributions | [52] | 315 |
SAMSeq (samr, 2.0) | (1) Default, non-parametric method based on Wilcoxon rank sum statistic | [19] | 140 |
PoissonSeq (1.1.2) | (1) Default, uses poisson log-linear model | [46] | 92 |
QuasiSeq (1.0.8) | Fits GLM with NB family. (1) QL, (2) QLShrink, (3) QLSPline | [34] | 57 |