Run the scconvert CLI for file-to-file conversion — scConvert_cli • scConvert

Performs file-to-file format conversion with three tiers:

C binary: HDF5 format pairs (h5ad, h5seurat, h5mu)
Streaming: zarr pairs (h5ad/h5seurat \(\leftrightarrow\) zarr) — copies fields directly without creating a Seurat intermediate
R hub: all other format pairs via scConvert()

Usage

scConvert_cli(
  input,
  output,
  assay = "RNA",
  gzip = 4L,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

input: Input file path
output: Output file path
assay: Assay name (passed as –assay)
gzip: Gzip compression level (0-9, passed as –gzip)
overwrite: If TRUE, remove output file before conversion
verbose: If TRUE, print CLI output

Value

TRUE on success, FALSE on failure

Details

Supported formats: h5ad, h5seurat, h5mu, loom, rds, zarr.