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

💻 ENiClust (Ensemble Integrative Clustering)

The source code for IC-subtypes prediction from whole-exome sequencing (WES) or genome sequencing (WGS) is available through GitHub repo and as a Docker image.

Run ENiClust using Docker:

docker run cancersysbio/eniclust-public:v2.1.0 ENiClust.py --help

Run ENiClust using Singularity:

singularity build eniclust.sif docker://cancersysbio/eniclust-public:v2.1.0

singularity exec eniclust.sif ENiClust.py --help

✔️ 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 [email protected] or Lise Mangiante [email protected] or Cristina Sotomayor-Vivas [email protected] or Alvina Adimoelja [email protected]