Urothelial Carcinoma Transcriptomic Analysis Pipeline and Figures

Reproducibility materials for a study on upper and lower tract urothelial carcinoma. The package contains an R-based analysis pipeline, figure-generation scripts, and all main and supplementary figures. It supports reproduction of differential expression analyses, Hallmark pathway scoring, and TCGA validation using data from GEO accessions GSE275638 and GSE133624.

Use Cases

• Reproduce paired differential expression analyses using the provided R scripts and raw data from GEO.
• Execute Hallmark pathway scoring and biological axis construction as defined in the pipeline.
• Validate findings against TCGA-BLCA data downloaded programmatically via TCGAbiolinks.
• Regenerate all main and supplementary figures (PNG format) using the included figure-generation scripts.

Strengths

• Includes the full R-based analysis pipeline for complete reproducibility.
• Contains all main and supplementary figures in PNG format.
• Well-documented with README files detailing the analysis steps.
• Raw input data sourced from established GEO accessions GSE275638 and GSE133624.

Limitations

• The 3.7 MB size indicates it is a code and figure repository, not the primary transcriptomic data files.
• Users must have R and specific packages installed to run the analysis pipeline.
• Direct analysis requires downloading raw data from external sources (GEO, TCGA) as described.

Provenance

Source

GEO accessions GSE275638 and GSE133624; TCGA-BLCA via TCGAbiolinks.

Collection Method

R-based computational analysis pipeline for transcriptomic data.

Time Range

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Freshness

Last updated March 13, 2026.

Geography

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