This repository contains all analysis scripts for the "The single-cell landscape of triple-negative breast cancer reveals a prognostic role of progenitor-like basoluminal tumor cells, Meyer et al., 2025".
DISCLAIMER: The manuscript associated with this code is in the peer-review process and thus the code will change accordingly. At this stage, it contains all code used for data presented in the manuscript but also exploratory data analysis parts. File paths have to be adjusted by the user.
The discovery/ directory contains all relevant data analysis scripts for IMC data analysis in the discovery cohort. It contains one sub-folder /other/ with support scripts.
The /validation/ directory contains all scripts for validation of findings (including scripts for mIF quantification / TCGA BRCA / MDACC / PDL1-IHC / scRNAseq organoid analysis).
Most scripts are written in the statistical programming language R. All R code was run with R version 4.3.2 (2023-10-31) on Ubuntu 20.04.4. Each .Rmd file contains a Software requirements section that lists all relevant packages for data analysis and processing. File paths have to be adjusted by the user.
Raw data is provided on zenodo (https://zenodo.org/records/10942609, https://zenodo.org/records/13691904]. Please note that, zenodo data access is currently restricted. Upon publication, all data and code will be made publicly available.