A framework for precision medicine in breast cancer. Calculates molecular subtype and provides pathway scores for samples individually.
Installation
To install the package run R and the following lines:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chronchi/ember")Basic usage
Check the tutorial page at chronchi.github.io/ember/
Citation
If you used the package (and enjoyed it!), use the following for citation:
Ronchi, C., Haider, S. & Brisken, C. EMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology. npj Breast Cancer 10, 56 (2024). https://doi.org/10.1038/s41523-024-00665-z
For the bibtex:
@article{Ronchi2024,
title = {EMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology},
volume = {10},
ISSN = {2374-4677},
url = {http://dx.doi.org/10.1038/s41523-024-00665-z},
DOI = {10.1038/s41523-024-00665-z},
number = {1},
journal = {npj Breast Cancer},
publisher = {Springer Science and Business Media LLC},
author = {Ronchi, Carlos and Haider, Syed and Brisken, Cathrin},
year = {2024},
month = jul
}