A survey of software for genome-wide discovery of differential splicing in RNA-Seq data

Table 1 Summary of differential splicing analysis software

	Model	Precision	Sensitivity	Pair end	Multicores	Novel events	Visualization	User-friendly	URL	Ref
Cuffdiff 2	Isoform	?	?	☺	☺	☺	☺	☺	[24]	[25]
MISO	Isoform	?	?	☺	☺	☹	☺	☺	[26]	[27]
DEXSeq	Exon	?	?	☹	☺	☹	☺	☹	[28]	[29]
DSGseq	Exon	?	?	☹	☹	☹	☹	☹	[30]	[31]
MATS	Junction + exon	☺☺	?	☺	☹	☺	☹	☺	[32]	[33]
DiffSplice	Junction + exon	?	?	☹	☹	☺	☺☺	☺	[34]	[35]
Splicing compass	Gene	?	?	☹	☺	☹	~	~	[36]	[37]
AltAnalyze (microarray)	Junction + exon	☺	☺☺	☹	☺	☹	☺	☺	[38]	[39]

Excellent (☺☺), very good (☺), good (~), could be improved (☹), unknown (?), multi-cores (supports use of multiple cores to speed computations).

ISSN: 1479-7364