README.md

Breast cancer genomic landscape

Code repository of publication: Complex rearrangements fuel ER+ and HER2+ breast tumours (Houlahan, Mangiante, Sotomayor-Vivas, Adimoelja et al., 2025)

📁 Repository content

This GitHub repository contains the following folders:

└─ analysis/: directory containing code used for data analysis
└─ data/: directory containing input data and source data to reproduce figures
|  └─ input_data/: input data
|  └─ source_data/: source data to reproduce figures
|     └─ extended_data/: source data for extended data figs
|     └─ figures/: source data for main figs
|     └─ supplementary_figure/: source data for supplementary figs
└─ extended_data/: directory code to reproduce extended data figs
└─ figures/: directory code to reproduce main figs
└─ supplementary_tables/: directory containing code to reproduce supplementary tables
└─ supplementary_figures/: directory containing R and other code to reproduce supplementary figures

✅ Citation

Kathleen E. Houlahan*, Lise Mangiante*, Cristina Sotomayor-Vivas*, Alvina Adimoelja*, Seongyeol Park, Aziz Khan, Sophia J. Pribus, Zhicheng Ma, Jennifer Caswell-Jin & Christina Curtis. Complex rearrangements fuel ER+ and HER2+ breast tumours, Nature (2025); doi: https://doi.org/10.1038/s41586-024-08377-x

✉️ Contact

For any questions, please contact Kathleen Houlahan khoulaha@stanford.edu or Lise Mangiante lisem@stanford.edu or Cristina Sotomayor-Vivas csotomv@stanford.edu or Alvina Adimoelja alvinaa@stanford.edu