Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

Simulation

The simulated dataset examples were in ./Simulation/simulated_datasets folder.

Brief descriptions of simulated scripts (./Simulation/Rcode folder):

simulated_Scenario1_low(middle,high).R: Integration data analysis for Scenario 1 with three different batch effects' scales.

simulated_Scenario2_low(middle,high).R: Integration data analysis for Scenario 2 with three different batch effects' scales.

simulated_Scenario3.R: Integrative data analysis for Scenario 3.

simulated_Scenario4.R: Integrative data analysis for Scenario 4.

simulated_Scenario5.R: Integrative data analysis for Scenario 5.

Real data analysis

Brief descriptions of real data analysis scripts (Real_data_analysis folder):

dorsolateral_prefrontal_cortex.R: Integration data analysis for human dorsolateral prefrontal cortex Visium data

mouse_liver.R: Integration data analysis for mouse liver ST data

olfactory_bulb.R: Integration data analysis for mouse olfactory bulb Slide-seqV2 data

hepatocellular_carcinoma.R: Integration data analysis for hepatocellular carcinoma Visium data

Real data results

The real data results were visualized with ggplot2 package (Real_data_results folder).

Brief descriptions of real data viualization scripts:

dorsolateral_prefrontal_cortex_viualize.R: Visualization for human dorsolateral prefrontal cortex Visium data

mouse_liver_viualize.R: Visualization for mouse liver ST data

olfactory_bulb_viualize.R: Visualization for mouse olfactory bulb Slide-seqV2 data

hepatocellular_carcinoma_viualize.R: Visualization for hepatocellular carcinoma Visium data