neighborhood/cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor

Spatial transcriptome cellular niche analysis using 10x xenium data go to There is a lung cancer and a breast cancer dataset. Let’s work on the lung cancer one. 37G zipped file! wget unzip sudo tar xvzf cell_feature_matrix.tar.gz cell_feature_matrix/ cell_feature_matrix/barcodes.tsv.gz cell_feature_matrix/features.tsv.gz cell_feature_matrix/matrix.mtx.gz read in the data with Seurat We really only care about the cell by gene count matrix which is inside the cell_feature_matrix folder, and the cell location x,y coordinates: cells.

How to construct a spatial object in Seurat

Sign up for my newsletter to not miss a post like this Single-cell spatial transcriptome data is a new and advanced technology that combines the study of individual cells’ genes and their location in a tissue to understand the complex cellular and molecular differences within it. This allows scientists to investigate how genes are expressed and how cells interact with each other with much greater detail than before.