Table 1.

Overview of the DS analysis methods used in the evaluation

Method	Version	Programming language used	Reference sequence used	Approach	Annotation	Experimental designs supported	Reference
Cufflinks/cuffdiff2	2.2.1	C++	Genome	isoform-based	Yes and de novo	Two groups	[16]
DiffSplice	0.1.2beta	C++	No	isoform-based	Ab initio	Two groups + blocking (1 factor)	[11]
DEXSeq	1.16.10	R/Bioconductor	Genome	exon-based	Yes	Complex designs	[18]
edgeR	3.12.1	R/Bioconductor	Genome	exon-based	Yes	Complex designs	[19]
JunctionSeq	1.3.4	R/Bioconductor	Genome	exon-based	Yes and de novo	Complex designs	[20]
limma	3.26.9	R/Bioconductor	Genome	exon-based	Yes	Complex designs	[21]
dSpliceType	2.0.0	Java	Genome	event-based	Yes	Two groups	[22]
MAJIQ	2.0	Python	Genome	event-based	Yes and de novo	Two groups	[23]
rMATS	3.2.2.beta/3.2.5	Python	Genome	event-based	Yes	Two groups, paired samples	[24]
SUPPA	2.0.0	Python	Transcriptome	event-based	Yes	Two groups, paired samples	[25]
SUPPA2	2.2.1	Python	Transcriptome	event-based	Yes	Two groups, paired samples	[26]