Skip to main content

Table 1 List of DE tools and pipelines along with their reference and number of citations

From: Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

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
  1. aAs reported by Web of Science (http://www.webofknowledge.com/; April 25, 2018). Further description about the pipelines can be found in the “Methods” section.
  2. Abbreviations: DF=degrees of freedom, GLM=generalized linear models, NB=negative binomial, QL=quasi-likelihood, QN=quantile normalization, QW=quality weight, VST=variance stabilizing transformation