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It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. The h5Seurat file format, based on HDF5, is on specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. This vignette serves as a guide to saving and loading Seurat objects to h5Seurat files.
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