Spatial Correlation of Gene Expressions

Codes for paper Modeling Spatial Correlation of Transcripts With Application to Developing Pancreas.

Process and Analyze Data

run train.py --path_file <path to data expression csv file> --path_nuc <Path to nuclei position csv file> --path_gene <Path to gene conversion csv file> --path_save <Path to save results>

By running train.py, the gene expression data are processed and the spatial correlation results are stored in a PKL file (as a SpatData class, defined in functions.model_spatdata).

Plot Results

How to access and visualize results is illustrated in

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