Converts an h5seurat file to AnnData zarr format, translating the h5seurat layout (levels/values factors, genes x cells CSC, reductions as cell.embeddings) to AnnData conventions (categories/codes, cells x genes CSR, obsm arrays). By default uses streaming that avoids a Seurat intermediate.
Usage
H5SeuratToZarr(
source,
dest,
assay = "RNA",
overwrite = FALSE,
gzip = 4L,
verbose = TRUE,
stream = TRUE
)Arguments
- source
Path to input .h5seurat file
- dest
Path for output .zarr directory
- assay
Assay name (default "RNA")
- overwrite
If TRUE, overwrite existing output
- gzip
Gzip compression level (0-9)
- verbose
Show progress messages
- stream
If TRUE (default), stream fields directly. If FALSE, load as Seurat then save as zarr.