API Reference

Multimodal omics

MuData([data, feature_types_names, as_view, ...])

Multimodal data object

Input/Output

to_anndata(mdata, **kwargs)	Convert MuData to AnnData by concatenating modalities.
to_mudata(adata, axis, by)	Convert AnnData to MuData by splitting it along obs or var.
concat(mdatas, *[, join, merge, uns_merge, ...])	Concatenates MuData objects.
read(filename, **kwargs)	Read an .h5mu formatted HDF5 file or a single modality inside it.
read_h5ad(filename, mod[, backed])	Read a modality from inside a .h5mu file or from a standalone .h5ad file (mod=None).
read_anndata(filename, mod[, backed])	Read a modality from inside a .h5mu file or from a standalone .h5ad file (mod=None).
read_h5mu(filename[, backed])	Read an .h5mu-formatted HDF5 file.
read_zarr(store)	Read from a hierarchical Zarr array store.
write(filename, data)	Write a MuData or AnnData object to an HDF5 file.
write_h5ad(filename, mod, data)	Write an AnnData object to an existing HDF5 file containing a MuData (an h5mu file).
write_anndata(filename, mod, data)	Write an AnnData object to an existing HDF5 file containing a MuData (an h5mu file).
write_h5mu(filename, mdata, **kwargs)	Write a MuData object to an HDF5 file.
write_zarr(store, data[, chunks, write_data])	Write a MuData or AnnData object to the Zarr store.

Extensions

register_mudata_namespace(name)

Decorator for registering custom functionality with a MuData object.

Types used by the former:

ExtensionNamespace(instance)

Protocol for extension namespaces.

Settings

set_options(**kwargs)

Control MuData options.