Data and code for constructing a custom single-cell RNA-sequencing reference for triple-negative breast cancer

This repository contains the preprocessing files, MATLAB preprocessing code, processed outputs, and additional data used to construct the custom single-cell RNA-sequencing reference and METABRIC bulk-expression mixture described in the "Identifying Therapeutic Targets ... " manuscript by Adams K, Bruner J, Ameziane S, Brown AN, Gbadamosi M, and Moore H. The single-cell reference was derived from the Wu et al. breast cancer scRNA-seq dataset, and the resulting reference was applied to selected Stage II, treatment-naive triple-negative breast cancer samples from METABRIC. The archive includes the files required to rerun TNBC_RNA_Seq_Main.m, the resulting CIBERSORTx input files, and the restricted METABRIC immune-cell deconvolution data used for initial-value calculations. See README_TNBC_RNASeq.md for details.