A highly resolved integrated single-cell atlas of HPV-negative Head and Neck Cancer
收藏NIAID Data Ecosystem2026-05-02 收录
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https://zenodo.org/record/14334994
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资源简介：
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(atlas@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)
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(atlas@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)
创建时间：
2024-12-30
