The DOI for the associated Zenodo data repostitory is 10.5281/zenodo.10729767 . Please download all data and follow below instructions for directory setup to execute code to reproduce figures.
MOUSE
Create a file for storing all mouse GeoMx data and where to set up your r project: Here named GeoMx_Mouse
GeoMx_Mouse/
R.proj
probe_data_mouse.rds
ACA_Profile_.csv
top_genesets_human
top_genesets_mu
kegg_brite_all_ENTREZID.gmt
Mos_Profile.csv
HUMAN
Create a file for storing all human GeoMx data and where to set up your r project: Here called GeoMx_Hu
GeoMx_Hu/
R.proj
probe_data_Hu.RDS
Profile_human_allreg.csv_profileMatrix.csv
top_genesets_human
top_genesets_mu
kegg_brite_all_ENTREZID.gmt
CosMx
Create a file for storing all CosMx data and where to set up your r project: Here called CosMx
CosMx/
seurat_object_3mon.rds
pSyn_positve_cells.csv
cohort_3mon.rds
astats_3mon.rds
To these directories, add the matching code from this github repsitory. The GeoMx files have an analysis and a matching helper function code while CosMx only has one file.
To run GeoMx code: load in all the helper functions to your environment first from teh helper fufnctions code, then use the analysis pipeline to produce figures.
DOI for this code repository is 10.5281/zenodo.10732492