Mapping intratumoral myeloid-T cell communication at single-cell resolution

This deposit contains the cell–cell communication networks and differential-abundance outputs supporting Bridges et al., "Mapping intratumoral myeloid–T cell communication at single-cell resolution." The networks were generated from a scRNA-seq dataset of CD45+ tumor-infiltrating immune cells in the YUMMER1.7 melanoma model, profiled across five treatment conditions (Control, anti-CD40 agonist, low-dose ICB, high-dose ICB, low-dose ICB + anti-CD40 agonist) and a d8/d10 time course of the combination therapy. A public MC38 dataset (GSE224400) is included as a cross-tumor comparator. Cell–cell interactions were inferred at single-cell resolution with NICHES (Raredon et al., 2023), and differential abundance of communication neighbourhoods between treatment conditions was tested with Milo (Dann et al., 2021) using replicate-level pseudo-bulks. The files released here are the AnnData (.h5ad) outputs that the analysis scripts in the companion GitHub repository load directly to produce all CCC-related figures in the manuscript. Raw 10x Genomics counts (the input to the NICHES pipeline) are deposited separately at NCBI GEO under accession GSE280374. All analysis code is at https://github.com/miller-jensen-lab/Bridgesetal-CCC and a paths-only configuration file (`config_paths.py`) maps each filename below to the figure(s) it produces.