This is a complimentary code for the paper: Cell specific priors rescue differential gene expression in spatial spot-based technologies
This repository contains all the code nesseccary to run your own simulation and analysis and reproduce the results and graph in the paper.
clone the code, and inside the script folder, you will find a python notebook with the full pipeline from simulations generations to graph creation.
The processed single cell reference file that was used to generate the simulation file is located under /simulation/reference_data/sc_lung_ref_filtered_a* It is cut to bits, in order to use it
In Linux: run the command: cat sc_lung_ref_filtered_* > sc_lung_ref_filtered.zip and then to unzip the file: unzip sc_lung_ref_filtered.zip
In Windows: copy /B sc_lung_ref_filtered_* sc_lung_ref_filtered.zip