Table 1. Methods for calling differentially expressed genes in RNA-seq data analysis.
Total citations were based on Google Scholar search result as of 22 September 2015, and normalized by number of years since formal publication. The methods were ranked according to their citations per year.
| Method | Total citations | Citations per year | Reference |
|---|---|---|---|
| DESeq* | 2,987 | 597 | Anders & Huber (2010) |
| edgeR* | 2,260 | 452 | Robinson, McCarthy & Smyth (2010) |
| Cuffdiff2 | 517 | 258 | Trapnell et al. (2013) |
| DESeq2* | 209 | 209 | Love, Huber & Anders (2014) |
| voom* | 143 | 143 | Law et al. (2014) |
| DEGseq | 592 | 118 | Wang et al. (2010) |
| NOISeq*,a,b | 324 | 81 | Tarazona et al. (2011) |
| baySeq | 310 | 62 | Hardcastle & Kelly (2010) |
| SAMSeqb | 114 | 57 | Li & Tibshirani (2013) |
| EBSeq | 107 | 53 | Leng et al. (2013) |
| PoissonSeq | 99 | 33 | Li et al. (2012) |
| BitSeq | 70 | 23 | Glaus, Honkela & Rattray (2012) |
| DSS | 46 | 23 | Wu, Wang & Wu (2013) |
| TSPM | 70 | 17 | Auer & Doerge (2011) |
| GPseq | 86 | 17 | Srivastava & Chen (2010) |
| NBPSeq | 65 | 16 | Di et al. (2011) |
| QuasiSeq | 47 | 16 | Lund et al. (2012) |
| GFOLD*,a | 44 | 15 | Feng et al. (2012) |
| ShrinkSeq | 30 | 15 | Van De Wiel et al. (2013) |
| NPEBseqb | 14 | 7 | Bi & Davuluri (2013) |
| ASC*,a | 32 | 6 | Wu et al. (2010) |
| BADGE | 2 | 1 | Gu et al. (2014) |
Notes.
*
Methods included in the present study.
a
Methods initially developed to analyze unreplicated RNA-seq data sets.
b
Non-parametric method.
Programming language: C/C+ + for GFOLD, Cuffdiff2 and BitSeq; Matlab for BADGE; R for the rest.