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 MuData object from HDF5 file or AnnData object (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 AnnData object from inside a .h5mu file or from a standalone .h5ad file
`read_h5ad`(filename, mod[, backed])	Read AnnData object from inside a .h5mu file or from a standalone .h5ad file
`read_h5mu`(filename[, backed])	Read MuData object from 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 MuData or AnnData to an HDF5 file
`write_anndata`(filename, mod, data)	Write AnnData object to the HDF5 file with a MuData container
`write_h5ad`(filename, mod, data)	Write AnnData object to the HDF5 file with a MuData container
`write_h5mu`(filename, mdata, **kwargs)	Write MuData object to the HDF5 file
`write_zarr`(store, data[, chunks, write_data])	Write MuData or AnnData object to the Zarr store