aksarkar / packages / mpebpm

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This package provides GPU-accelerated inference for the Empirical Bayes Poisson Means (EBPM) problem. This model can be used to model variation in scRNA-seq data due to measurement error, as well as variation in true gene expression values (Sarkar and Stephens 2020). This implementation readily supports fitting the model for data on the order of 10^6 cells and 10^4 genes in parallel. It also supports fitting multiple EBPM problems per gene in parallel, as arise when e.g., cells have been assigned to groups (clusters). For example, we have used the method to solve 537,678 EBPM problems (54 conditions by 9,957 genes) in parallel in a few minutes (Sarkar et al. 2019).

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