This example data was generated from the mouse embryo spatial transcriptomics dataset of 3 mouse embryos, with 351 genes and a total of 57536 cells. For running examples, we subset the data by selecting 1000 random cells from embryo 2, excluding any cells annotated as 'low quality'. After subsetting, we have 1000 cells from embryo 2 and 351 genes.
Usage
data(example)Format
spe a spatialExperiment object containing gene expression matrix with
normalised counts, where rows indicate genes and columns indicate cells. Also,
contains a data frame of cell metadata including cell IDs, sample IDs, cell
type annotations, and x-y coordinates of cells.
nnCells a matrix where each row corresponds to a cell in spe object,
and the columns correspond to the nearest neighbors.
regXclust a list where each element corresponds to a cell in spe
object, and contains the cluster composition proportions.
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