Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease

This repository contains the preprocessed single-cell RNA data from the manuscript Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease (Zhang & Allen et al. PLOS ONE 2026). Data Descriptions: BAL_FINAL.rds Seurat Object with the entire dataset BAL_FINAL.h5ad Scanpy Object with the entire dataset BAL_FINAL_META.txt Metadata for each cell mlm_umap_embeddings.csv UMAP embeddings for the monocyte-derived clusters mlm_cluster_metadata.csv Monocyte-derived macrophage metadata monomacs_only.rds Seurat Object with monocyte-like macrophages (MLMs) ipf_allen2022.full_score.gz scDRS results for each cell using the Richard Allen et al. 2022 IPF GWAS summary statistics