SeuratDisk: Interfaces for HDF5-Based Single Cell File Formats

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.

Package options

SeuratDisk uses the following options to control behaviour, users can configure these with options:

SeuratDisk.dtypes.logical_to_int

When writing logical vectors, coerce to integer types to ensure compatibility across languages (see BoolToInt for more details)

SeuratDisk.dtypes.dataframe_as_group

When writing data.frames, always write out as a group regardless of factor presence

SeuratDisk.chunking.MARGIN

Default direction for chunking datasets; choose from:

largest

Chunk along the largest dimension of a dataset

smallest

Chunk along the smallest dimension

first

Chunk along the first dimension

last

Chunk along the last dimension

See also

Useful links:

• https://mojaveazure.github.io/seurat-disk/

• https://github.com/mojaveazure/seurat-disk

• Report bugs at https://github.com/mojaveazure/seurat-disk/issues