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

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

Tool (package version)	Pipelines	Reference	Citations^a
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

^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.
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

ISSN: 1474-760X