Table 1.

Information on 29 R packages, methods, or pipelines, for DE analysis of RNA-Seq data: the number of citations of the article introducing the method (until October 2017, extracted from All Databases of Web of Science^a), the used probabilistic model, the default normalization method, and whether or not a Bayesian approach is considered.

R-package or method	References	December, 2013	January, 2015	January, 2016	January, 2017	October, 2017	October, 2017 (%)	Distribution	Normalization	Bayesian
edgeR	Robinson et al., 2010	430	982	1,854	3,040	4,450	22.00	Negative binomial	TMM	No
Cufflinks (Cuffdiff)	Trapnell et al., 2010	861	1,648	2,446	3,300	4,283	21.17	Poisson	FPKM (geometric)	Yes
DESeq	Anders and Huber, 2010	607	1,395	2,299	3,167	4,157	20.55	Negative binomial	RLE	No
DESeq2	Love et al., 2014			83	282	1,899	9.39	Negative binomial	RLE	Yes
vst or QN + limma	Ritchie et al., 2015					1,276	6.31	Gaussian	vst or QN	Yes
Cuffdiff 2	Trapnell et al., 2013			421	699	950	4.70	Beta negative binomial	Geometric	No
DEGSeq	Wang et al., 2010	178	297	458	636	850	4.20	Poisson	Total count	No
voom + limma	Law et al., 2014					493	2.44	Gaussian	log-CPM	Yes
NOISeq	Tarazona et al., 2011	65	164	263	377	473	2.34	Non-parametric	CPM	No
baySeq	Hardcastle and Kelly, 2010	72	109	178	232	302	1.49	Negative binomial	Total count	Yes
EBSeq	Leng et al., 2013	5	31	93	170	270	1.33	Negative binomial	RLE	Yes
Myrna	Langmead et al., 2010	57	88	112	117	149	0.74	Poisson or Gaussian	3rd quartile	No
SAMseq	Li and Tibshirani, 2013	0	22	52	91	129	0.64	Non-parametric	Trimmed total count	No
GFOLD	Feng et al., 2012			41	73	93	0.46	Hierarchical Poisson	RLE	Yes
PoissonSeq	Li et al., 2012	4	19	43	63	88	0.44	Poisson	Trimmed total count	No
DSS	Wu et al., 2013			31	44	61	0.30	Gamma-Poisson	3rd quartile	Yes
BBSeq	Zhou et al., 2011	15	21	30	40	50	0.25	Beta-binomial	Total count	No
QuasiSeq	Lund et al., 2012					42	0.21	Negative binomial	3rd quartile	No
TSPM	Auer and Doerge, 2011	8	12	16	26	39	0.19	Two-stage Poisson	Total count	No
ShrinkSeq	Wiel et al., 2013	5	14	18	28	33	0.16	Zero-inflated negative binomial	None	Yes
GENE-counter	Cumbie et al., 2011	9	14	20	26	30	0.15	Negative binomial	Total count	No
NBPSeq	Di et al., 2011	11	14	21	23	28	0.14	Negative binomial	Total count	No
sSeq	Yu et al., 2013					27	0.13	Negative binomial	RLE	No
Polyfit	Burden et al., 2014					15	0.07	Negative binomial	RLE	No
NPEBseq	Bi and Davuluri, 2013	0	4	11	12	14	0.07	Gamma-Poisson	TMM	Yes
BMDE	Lee et al., 2011	4	5	8	8	10	0.05	Binomial (position-level)	Total count	Yes
LFCseq	Lin et al., 2014					6	0.03	Non-parametric	Trimmed total count	No
CEDER	Wan and Sun, 2012	0	1	2	4	5	0.02	Negative binomial	RLE	No
ShrinkBayes	van de Wiel et al., 2014			1	3	5	0.02	Zero-inflated negative binomial	None	Yes

^ahttp://apps.webofknowledge.com