Symphony objects containing single-cell embeddings for PBMC-blood dataset

Symphony objects containing cell state embedding for each cell type using cells from PBMC-blood alone (Kang et al. Nat Gen 2023). For each cell type separately, we performed normalization, variable gene selection, PCA, Harmony integration, UMAP, and Symphony reference creation using the script: https://github.com/immunogenomics/hla2023/blob/main/scripts/4_sceQTL/0_symphony_integration_OneK1K_pool.REach reference object contains:meta_data: cell metadatavargenes: variable genes, means, and standard deviations used for scalingloadings: gene loadings for projection into pre-Harmony PC spaceR: Soft cluster assignmentsZ_orig: Pre-Harmony PC embeddingZ_corr: Harmonized PC embeddingcentroids: locations of final Harmony soft cluster centroidscache: pre-calculated reference-dependent portions of the mixture modelumap: UMAP coordinatessave_uwot_path: path to saved uwot model (for query UMAP projection into reference UMAP coordinates)normalization_method: type of normalization used