Code related to the manuscript 'Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids' Nature Microbiology 2023.
You can run the notebook using the data files from the related GEO repository GSE 163952 starting from the alignment files or directly from the pre-processed Seurat objects (recommended). In the latter case, please ignore the code before the import of the pre-processed object with the readRDS function.