This repository includes scripts for the results generated in:
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Folder 01-Regional_data_processing/ includes the scripts to further process the RNA data including cell type annotations and figure generating scripts to plot tSNE / marker genes
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Folder 02-ATAC_processing/ includes the scripts to further process the ATAC data
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Folder 03-DE_analysis/ includes the scripts to run DEG analysis on the RNA data
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Folder 04-ATAC_DE/ includes the scripts to run ATAC DE analysis
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Folder 05-communication/ includes the scripts to run cell-cell communication analysis
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Folder 06-/astrocyte/ includes the scripts for astrocyte analysis
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Folder 07-/Viral_Detection includes the scripts to run viral detection
Code to run the nextflow pipeline can be found here: https://github.com/kragrawa/scorch_pipeline_dev