The h5Seurat file format is 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. 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. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.
SeuratDisk uses the following options to control behaviour, users can configure
When writing data.frames, always write out as a group regardless of factor presence
Default direction for chunking datasets; choose from:
Chunk along the largest dimension of a dataset
Chunk along the smallest dimension
Chunk along the first dimension
Chunk along the last dimension