This dataset contains spatial transcriptomics data from 3 mouse embryos, with 351 genes and a total of 57536 cells. For vignettes, we subset the data by randomly selecting 5000 cells from embryo 2, excluding cells that were annotated as 'low quality'.
Usage
data(mEmbryo2)Format
me_expr a gene expression matrix with normalised counts, where rows
indicate genes and columns indicate cells.
me_data a data frame of cell metadata including cell IDs, sample IDs,
cell type annotations, and x-y coordinates of cells.
Source
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis, Nature Biotechnology, 2021. Webpage: https://www.nature.com/articles/s41587-021-01006-2