Table 3.

Comparative summary of five computational approaches used to study splicing in single-cell RNAseq

	SingleSplice [42]	MISO [41]	BRIE [43]	Expedition [38]	RSEM [73]
Observation level	Gene	Exon	Exon	Exon	Isoform (full transcript)
Measure of expression	Differentially alternatively spliced (yes/no)	PSI	PSI	PSI	Read counts per isoform
Single-cell specific	✓	✗	✓	✓	?
Includes interpretation of changes	✓	✗	✗	✓	✗

PSI percentage spliced-in, RSEM RNA-seq by expectation maximization