A highly resolved integrated single-cell atlas of HPV-negative Head and Neck Cancer

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([e-mail][[e-mail]$Compartment == "Immune",]))immune[["umap"]]@cell.embeddings <- as.matrix([e-mail][,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")])colnames(x = immune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2) nonimmune <- subset(atlas, cells = rownames([e-mail][[e-mail]$Compartment == "nonImmune",]))nonimmune[["umap"]]@cell.embeddings <- as.matrix([e-mail][,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")])colnames(x = nonimmune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2)本数据集为人乳头瘤病毒（HPV）阴性头颈鳞状细胞癌单细胞转录组图谱。 该图谱以Seurat（v4.1.0）对象的形式存储为.rds格式文件，可在R语言环境中加载。 可通过以下代码将数据加载至R语言环境： atlas <- readRDS('FullHNSCCAtlas.rds') 可通过如下代码分离免疫组分与非免疫组分： immune <- subset(atlas, cells = rownames([e-mail][[e-mail]$Compartment == "Immune",])) immune[["umap"]]@cell.embeddings <- as.matrix([e-mail][,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")]) colnames(x = immune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2) nonimmune <- subset(atlas, cells = rownames([e-mail][[e-mail]$Compartment == "nonImmune",])) nonimmune[["umap"]]@cell.embeddings <- as.matrix([e-mail][,c("CompartmentUMAP1_Coordinates", "CompartmentUMAP2_Coordinates")]) colnames(x = nonimmune[["umap"]]@cell.embeddings) <- paste0("UMAP_", 1:2)