An example dataset
Format
Visium_human_DLPFC
A list with 3 elements
- counts
Gene expression count matrix. Rows and columns indicate genes and spots, respectively.
- spatial_coords
Spatial coordinates matrix. Rows indicate spots.
- cell_type_proportions
Cell type proportion matrix estimated by RCTD. Rows and columns indicate spots and cell types, respectively.
Source
Visium human dorsolateral prefrontal cortex (DLPFC) sample 151673. The count matrix and spatial coordinates were obtained via the spatialLIBD resource (https://research.libd.org/spatialLIBD/) and were originally generated and described in Maynard KR, Collado-Torres L, Weber LM, et al. (2021) Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience 24, 425–436. doi:10.1038/s41593-020-00787-0 . Cell type proportions were estimated by the authors of this package using RCTD with a reference dataset (https://brukerspatialbiology.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/human-frontal-cortex-ffpe-dataset/) as the single-cell reference.
This dataset is redistributed here for illustration only. It is not covered by the package license and remains subject to the terms of the original data providers. Please cite Maynard et al. (2021) when using it.