nsclc_manuscript_2023

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:

1. COMMOT.ipynb. Ligand receptor analysis in MERFISH data, restricted to cells in the immunity hubs.
2. Figures.ipynb. Code to reproduce figures in the manuscript.
3. LungCellsAbundance.ipynb. Enrichment analysis for which cell types are in which types of spatial hubs.
4. IntraHubLocalization.ipynb. Spatial colocalization analysis of cell types within hubs.
5. LungCellsInHubs.ipynb. Labeled coarse cell types in MERFISH data, after segmentation.
6. LungCellsInHubs_ImmuneFineTyping.ipynb. Labeled fine-grained cell types and states for immune cells in MERFISH data.
7. LungNicheDiscovery.ipynb. Identified and labeled spatial hubs using spatial tiling of transcripts.
8. fibroblasts.ipynb. Analysis of stromal MERFISH cells, including fine-grained annotation and localization within hubs.
9. geomx.ipynb. All analysis of geomx data.