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.
• GSE224986: Single cell libraries.
• GSE228332: Bulk RNA-seq validation experiments.

Contributors

• First Author: Yihan Wang Yihan.Wang@UTSouthwestern.edu
• Corresponding Author: Gary Hon Gary.Hon@UTSouthwestern.edu