Reproducibility materials for: Continuous biological divergence between upper and lower tract urothelial carcinoma revealed by paired pathway-level transcriptomic analysis

Reproducibility materials for the manuscript “Continuous biological divergence between upper and lower tract urothelial carcinoma revealed by paired pathway-level transcriptomic analysis”. This item contains the full R-based analysis pipeline, figure-generation scripts, README documentation, and all main and supplementary figures. The repository supports reproduction of paired differential expression analyses, Hallmark pathway scoring, biological axis construction, bootstrap sensitivity analyses, and TCGA validation. Raw input data are obtained from GEO accessions GSE275638 and GSE133624, while TCGA-BLCA data are downloaded programmatically via TCGAbiolinks, as described in the included README.