Input/Output

Backed AnnData objects

AnnData(*, filename, X, n_obs, n_vars, obs, ...)	An annotated data matrix.
AnnDataSet(*, adatas, filename, add_key)	Similar to AnnData, AnnDataSet contains annotations of observations obs (obsm, obsp), variables var (varm, varp), and unstructured annotations uns.

AnnData IO

read(filename, backed, /)	Read .h5ad-formatted hdf5 file.
read_mtx(mtx_file, file, sorted)	Read Matrix Market file.
read_10x_mtx(path, storage[, prefix])	Read 10x-Genomics-formatted mtx directory.
read_csv(csv_file, file, has_header, ...)
read_dataset(filename, ...)	Read AnnDataSet object.
AnnData.write(filename)	Write .h5ad-formatted hdf5 file.
AnnData.subset(obs_indices, var_indices, out)	Subsetting the AnnData object.
AnnData.copy(filename)	Copy the AnnData object.
AnnDataSet.subset(obs_indices, var_indices, out)	Subsetting the AnnDataSet object.
AnnDataSet.copy(dirname)	Copy the AnnDataSet object to a new location.