This repository contains all analysis scripts for the triple negative breast cancer IMC study from Meyer et al., 2024.
DISCLAIMER: The manuscript associated with this code is in the peer-review process and thus the code will change accordingly.
The discovery/ directory contains all relevant data analysis scripts for IMC data analysis in the discovery cohort. It contains one sub-folder /metadata/ with scripts for clinical metadata annotation.
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.
Upon publication, the raw data associated with this repository will available on zenodo or from the respective original research articles.