A highly resolved integrated single-cell atlas of HPV-negative Head and Neck Cancer
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A single cell transcriptomic atlas of HPV-negative Head and Neck Squamous Carcinomas. The atlas is a Seurat (v 4.1.0) object stored as a .rds file, which can be loaded in R. The data can be loaded into R as follows: atlas <- readRDS('FullHNSCCAtlas.rds') The immune and nonimmune compartments can be separated as follows: immune <- subset(atlas, cells = rownames(comb1@meta.data[atlas@meta.data$Compartment == "Immune",]))immune[["umap"]]@cell.embeddings <- as.matrix(immune@meta.data[,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")])colnames(x = immune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2) nonimmune <- subset(atlas, cells = rownames(atlas@meta.data[atlas@meta.data$Compartment == "nonImmune",]))nonimmune[["umap"]]@cell.embeddings <- as.matrix(nonimmune@meta.data[,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")])colnames(x = nonimmune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2)
