This includes all of the code for the manuscript "A comprehensive single-cell breast tumor atlas defines cancer epithelial and immune cell heterogeneity and interactions predicting anti-PD-1 therapy response" (https://doi.org/10.1016/j.xcrm.2024.101511).
The integrated primary breast tumor atlas may be downloaded at https://zenodo.org/records/10672250 (contains matrix, genes, barcodes, metadata files).
Here is a breakdown of the file tree:
1. **Preprocessing:** Contains the code for setting up and building the datasets, broken down based on technology type (scRNA-seq, bulk RNA-seq).
- bulkRNA: Includes subfolders for The Cancer Genome Atlas (TCGA), I-SPY2, and Cancer Cell Line Encyclopedia (CCLE) datasets.
- scRNA: Includes subfolders for the integrated primary breast tumor atlas and Bassez et al. (anti-PD-1-treated) datasets.
- spatial: Includes code for loading of Visium spatial datasets from Wu et al. 2021 and 10x Genomics.
2. **Analysis**: Contains the code to generate all of the main figures in https://doi.org/10.1016/j.xcrm.2024.101511.
- Figure 1: Creation of integrated primary breast tumor atlas and identification of NK cell subsets
- Figure 2: Analysis of cancer epithelial cell intratumoral transcriptional heterogeneity, focusing on ERBB2/HER2 and TACSTD/TROP2
- Figure 3: Identification of 10 GEs to define cancer epithelial cell heterogeneity and immune cell interactions
- Figure 4: Development of InteractPrint based on GE-immune interaction and predicting response to anti-PD-1 therapy