API reference#

Multimodal omics #

`muon.MuData`([data, feature_types_names, ...])	Multimodal data object
`muon.pp`
`muon.tl`
`muon.pl`
`muon.utils`

`initialise_default_files`(data, path)	Locate default files for ATAC-seq
`read`(filename, **kwargs)	Read an .h5mu formatted HDF5 file or a single modality inside it.
`read_10x_h5`(filename[, extended])	Read data from 10X Genomics-formatted HDF5 file
`read_10x_mtx`(path[, extended])	Read data from 10X Genomics-formatted files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz)
`read_anndata`(filename, mod[, backed])	Read a modality from inside a .h5mu file or from a standalone .h5ad file (mod=None).
`read_elem`(elem)	Read an element from a store.
`read_h5ad`(filename, mod[, backed])	Read a modality from inside a .h5mu file or from a standalone .h5ad file (mod=None).
`read_h5ad_dataframe`(group)	Backwards compat function
`read_h5mu`(filename[, backed])	Read an .h5mu-formatted HDF5 file.
`read_zarr`(store)	Read from a hierarchical Zarr array store.
`warn`	Issue a warning, or maybe ignore it or raise an exception.
`write`(filename, data)	Write a `MuData` or `AnnData` object to an HDF5 file.
`write_anndata`(filename, mod, data)	Write an AnnData object to an existing HDF5 file containing a MuData (an h5mu file).
`write_elem`(store, k, elem, *[, dataset_kwargs])	Write an element to a storage group using anndata encoding.
`write_h5ad`(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.