Overview

This repository contains the jupyter lab notebooks of analysis and plotting after performing pySpade analysis of breast cancer associated enhancers perturbations.

Link to pySpade

Requirement

• Python (3.7 +)
• Numpy (1.16 +)
• Pandas (0.25 +)
• Scipy (1.1 +)
• Matplotlib (3.3 +)
• pyCircos (0.3.0 +)

Fastq files

• [GSE223812]: Bulk ATAC-seq of breast cancer cell lines. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223812)
• [GSE224986]: Single cell libraries. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224986)
• [GSE228332]: Bulk RNA-seq validation experiments. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228332)

How to cite

Wang, Y. et al. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. Genome Biol 26, 10 (2025). Link to paper

Contacts

• Yihan Wang Yihan.Wang@UTSouthwestern.edu
• Gary Hon Gary.Hon@UTSouthwestern.edu