anndata.h5py

Wraps h5py to handle sparse matrices.

anndata.h5py is based on and uses the conventions of h5sparse by Appier Inc.. See the copyright and license note in the source code.

The design choices of anndata.h5py, however, are different. In particular, anndata.h5py allows handling sparse and non-sparse data at the same time. It achieves this by extending the functionality of File and Group objects in the h5py API, and by providing a new SparseDataset object.

For examples and further information, see this blog post.

File(name[, mode, driver, libver, …]) Like h5py.File, but able to handle sparse matrices.
Group(h5py_group[, force_dense]) Like h5py.Group, but able to handle sparse matrices.
Dataset Equivalent to h5py.Dataset.
SparseDataset(h5py_group) Analogous to h5py.Dataset, but for sparse matrices.