Code used in the analysis of "Human lung cancer harbors spatially-organized stem-immunity hubs associated with response to immunotherapy" Chen et al Nature Immunology 2024
The notebooks included, in no particular order:
- COMMOT.ipynb. Ligand receptor analysis in MERFISH data, restricted to cells in the immunity hubs.
- Figures.ipynb. Code to reproduce figures in the manuscript.
- LungCellsAbundance.ipynb. Enrichment analysis for which cell types are in which types of spatial hubs.
- IntraHubLocalization.ipynb. Spatial colocalization analysis of cell types within hubs.
- LungCellsInHubs.ipynb. Labeled coarse cell types in MERFISH data, after segmentation.
- LungCellsInHubs_ImmuneFineTyping.ipynb. Labeled fine-grained cell types and states for immune cells in MERFISH data.
- LungNicheDiscovery.ipynb. Identified and labeled spatial hubs using spatial tiling of transcripts.
- fibroblasts.ipynb. Analysis of stromal MERFISH cells, including fine-grained annotation and localization within hubs.
- geomx.ipynb. All analysis of geomx data.