srtdisk: Extended HDF5-Based Single Cell File Format Support

Extended implementation of SeuratDisk for Seurat v5. Provides interfaces for HDF5-based single-cell file formats including h5Seurat and AnnData (h5ad) with enhanced support for Seurat v5 Assay5 and spatial data.

Package options

srtdisk uses the following options to control behavior, 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

SeuratDisk.dimreducs.allglobal

Treat all DimReducs as global, regardless of actual global status

SeuratDisk.compression.level

Gzip compression level for HDF5 dataset writes (0-9). Level 0 means no compression, level 4 (default) is a good balance of speed vs size. Only applies to newly created datasets, not to data copied via obj_copy_from.

See also

Useful links:

• https://mianaz.github.io/srtdisk/

• https://github.com/mianaz/srtdisk

• Report bugs at https://github.com/mianaz/srtdisk/issues

Author

Maintainer: Miana Z zzeng4@nd.edu

Authors:

• Paul Hoffman phoffman@nygenome.org (ORCID)

• Rahul Satija rsatija@nygenome.org (ORCID)