conveRtainer

Docker containers + scripts for file conversions.

Seurat to h5ad

Converts an serialized Seurat object from RDS to h5ad (anndata), compatible with cellxgene. The new file will appear in the same location with an .h5ad suffix.

./seurat_to_h5ad <RDS-FILE>

Seurat to zarr

Converts an serialized Seurat object from RDS to ZARR, compatible with vitessce. The new files will appear in a new folder in the same location with an .h5ad.zarr suffix.

./seurat_to_zarr <RDS-FILE>

h5ad to zarr

Converts an serialized an anndata h5ad dataset to ZARR, compatible with vitessce. The new files will appear in a new folder in the same location with an .zarr suffix.

./h5ad_to_zarr <H5AD-FILE>