Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section

DOI: 10.5281/zenodo.21497736 Files single_nuclei.tar (~31 GB) → data/single_nuclei/ spatial_spaceranger.tar (~29 GB) → data/spatial/spaceranger/ spatial_r_objects.tar (~14 GB) → data/spatial/r_objects/ spatial_xenium.tar (~8 GB) → data/spatial/xenium/ other.tar (~6 GB) → data/other/ figs.tar (~9 GB) → figs/ Spatial data is split by subdirectory (content-based). Extracting all three spatial archives into the same place rebuilds data/spatial/ with no conflicts. No cat/split reassembly. Setup recipe (from the repository root) # Data archives contain single_nuclei/, spatial/, or other/ at the top level tar -xf single_nuclei.tar -C data/ tar -xf other.tar -C data/ tar -xf spatial_spaceranger.tar -C data/ tar -xf spatial_r_objects.tar -C data/ tar -xf spatial_xenium.tar -C data/ # Figures: archive contains figs/ at the top level tar -xf figs.tar cp sample_metadata.csv data/ Environment setup and notebooks live in the GitHub repository (bash environment/setup.sh, then conda activate simplex).