From: Impact of human gene annotations on RNA-seq differential expression analysis
Tool | Abbrv. ∗1 | Version | Category ∗2 | #Citations ∗3 | References | Year |
---|---|---|---|---|---|---|
TopHat2 | Th | 2.1.1 | alignment | 11740 | 2009 (ver.1), 2013 (ver.2) | |
STAR | Sr | 2.6.1d | alignment | 5443 | [28] | 2013 |
HISAT | Hs | 2.1.0 | alignment | 1799 | 2015 (ver.1), 2019 (ver.2) | |
Cufflinks | Cu | 2.2.1 | assembly, quantification, DE | 8102 | 2010 (ver.1), 2013 (ver.2) | |
RSEM | Rs | 1.3.1 | quantification | 4335 | [25] | 2011 |
StringTie | St | 2.0.6 | assembly, quantification | 721 | [39] | 2015 |
Kallisto | Ka | 0.46.1 | quantification | 312 | [40] | 2016 |
Salmon | Sa | 1.5.0 | quantification | 517 | [41] | 2017 |
DESeq2 | De | 1.26.0 | DE | 6865 | 2010 (ver.1), 2014 (ver.2) | |
EBSeq | Eb | 1.26.0 | DE | 468 | [44] | 2013 |
Ballgown | Ba | 2.18.0 | DE | 102 | [45] | 2015 |
Sleuth | Sl | 0.30.0 | DE | 170 | [46] | 2017 |