Single-cell RNAseq dataset to demonstrate the use of NicheNet directly on a Seurat object. The data came from "Medaglia et al. Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq, Science 2017". This data was generated via the NICHE-seq method to characterize immune cell composition in the T cell area of inguinal lymph nodes, both in steady-state and 72 hours after lymphocytic choriomeningitis virus (LCMV) infection. The Seurat objects contain the aggregated data after applying the Seurat alignment pipeline. seuratObj.rds: full dataset seuratObj_test.rds: dataset with reduced size (only highly variable genes and CD8 T cells and monocytes)

{"references": ["Medaglia et al. Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq, Science 2017"]}