Workflow from Scientific Research

Overview of data simulation: To simulate realistic ST data, we take a real ST dataset and perform deconvolution to calculate the expected expression vector for each spot {X}_{s} . To generate data in the absence of niche effects, we simulate expression vectors from a negative binomial distribution with mean {X}_{s} and overdispersion parameter 1. To generate data with niche effects, we specify {beta}_{i,n} for all index-niche pairs (i,n) and calculate the new expected expression vector for each spot {Y}_{s} based on the niche-DE model. We then simulate expression vectors from a negative binomial distribution with mean {Y}_{s} and overdispersion parameter 1. We also simulate ST data in the presence of spatial bleeding by calculating new expression vectors based on the SpotClean model with local bleeding parameter 0.25. Afterwards, we calculate the type 1 error rate, power, and runtime of niche-DE.

DOI