. Author manuscript; available in PMC: 2021 Dec 1.

Published in final edited form as: Nat Genet. 2021 May 24;53(6):770–777. doi: 10.1038/s41588-021-00873-4

Table 2. Multi-gene models for scRNA-seq data.

Multi-gene models partition variation in true expression into structured and stochastic components. The link function describes a transformation, and the noise distribution indicates an assumption about the stochastic component (p(u_ij) in (3)). Method indicates previously published methods and software packages that use the corresponding observation model to analyze data.

Link function	Noise distribution	Method
Identity	None	NMF⁴⁸, scHPF⁴⁹
Identity	Gamma	NBMF⁵⁰
log	None	GLM-PCA¹⁹
log	Gamma	scNBMF⁵¹, GLM-PCA¹⁹
log	Point-Gamma	ZINB-WaVE⁵²
Neural network	Point-Gamma	scVI²⁹, DCA²¹