Notebooks used to produce results for spatial transcriptomics analysis presented in the publication "FAP-Targeted LTBR Agonist Drives HEV Differentiation and Immune Niche Formation for Improved Immunotherapy Response in Solid Tumours"
Primary Processing:
- 00_Quality_Control.ipynb
- 03_SampleIntegration_Clustering.ipynb
Differential expression analysis and pathway enrichment analysis:
- 07_Pseudobulk_analysis.ipynb
- 07_Pseudobulk_analysis-perRegion.ipynb
ScRNA-seq based deconvolution and downstream analyses:
- 08_Deconvolution_C2L.ipynb
- 08_03_Deconvolution_C2L_Proportions-updated.ipynb
- 08_y_Deconvolution_C2L_Downstream_Coloc_EnrichAnnotations-updated.ipynb
- 13_TargetExpressionExploration.ipynb