SLFN11 Figure

This repository generates SLFN11 expression figures from TCGA and GTEx Toil/Xena RNA-seq data.

Outputs

The publication figures are written to results/:

• slfn11_pan_cancer_violin_log2TPM.png
• slfn11_pan_cancer_violin_tpm.png
• slfn11_tcga_tumor_vs_normal.png
• slfn11_gtex_tissues.png
• slfn11_matched_tcga_gtex.png

Raw downloaded data are cached in results/raw/ and intentionally excluded from git.

Requirements

Install the Python dependencies:

pip install -r requirements.txt

On Windows, use py -m pip install -r requirements.txt if python is not on PATH.

Usage

Run the analysis from the repository root:

python script.py

On Windows, use py script.py if needed.

On the first run, the script downloads TCGA and GTEx expression and phenotype tables into results/raw/. Later runs reuse those files if present.

Data Sources

Expression and phenotype data are downloaded from the UCSC Xena Toil recompute datasets:

• TCGA TPM matrix: tcga_RSEM_gene_tpm.gz
• GTEx TPM matrix: gtex_RSEM_gene_tpm.gz
• TCGA/TARGET/GTEx phenotype table: TcgaTargetGTEX_phenotype.txt.gz
• GTEx phenotype table: GTEX_phenotype.gz