A highly resolved integrated single-cell atlas of HPV-negative Head and Neck Cancer
Description
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)
Files
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Additional details
Funding
- National Institute of Dental and Craniofacial Research
- System-Level Analyses of Multi-Omics Data to Reveal Mechanisms of Head & Neck Cancer R01DE031831
- National Institute of Dental and Craniofacial Research
- Defining immune-evasive mechanical signaling in head and neck cancer R01DE033519
- National Institute of Dental and Craniofacial Research
- Elucidating mechanisms of cellular communication critical for head and neck cancer progression and metastasis. 1F31DE033292-01
Software
- Repository URL
- https://github.com/montilab/kroehling_et_al_hpvneg_hnscc_atlas
- Programming language
- R