scqtl
This package implements maximum likelihood estimation of the zero-inflated negative binomial model described in: Abhishek K Sarkar, Po-Yuan Tung, John D. Blischak, Jonathan E. Burnett, Yang I. Li, Matthew Stephens, Yoav Gilad. "Discovery and characterization of variance QTLs in human induced pluripotent stem cells". PLoS Genetics (2019). https://doi.org/10.1371/journal.pgen.1008045 The key idea is that we learn latent point-Gamma distributions for expression per individual/condition per gene, and then perform all downstream analysis on (the parameters of) those distributions.