API

The central class:

AnnData([X, obs, var, uns, obsm, varm, …])

An annotated data matrix.

Reading

Reading anndata’s native file format .h5ad.

read_h5ad(filename[, backed, as_sparse, …])

Read .h5ad-formatted hdf5 file.

Reading other file formats.

read_csv(filename[, delimiter, …])	Read .csv file.
read_excel(filename, sheet[, dtype])	Read .xlsx (Excel) file.
read_hdf(filename, key)	Read .h5 (hdf5) file.
read_loom(filename[, sparse, cleanup, …])	Read .loom-formatted hdf5 file.
read_mtx(filename[, dtype])	Read .mtx file.
read_text(filename[, delimiter, …])	Read .txt, .tab, .data (text) file.
read_umi_tools(filename[, dtype])	Read a gzipped condensed count matrix from umi_tools.
read_zarr(store)	Read from a hierarchical Zarr array store.

Writing

Writing to anndata’s native file format .h5ad.

AnnData.write([filename, compression, …])

Write .h5ad-formatted hdf5 file.

Writing to other formats.

AnnData.write_csvs(dirname[, skip_data, sep])	Write annotation to .csv files.
AnnData.write_loom(filename[, write_obsm_varm])	Write .loom-formatted hdf5 file.
AnnData.write_zarr(store[, chunks])	Write a hierarchical Zarr array store.

h5py

Independent of AnnData, the submodule anndata.h5py provides a thin wrapper of h5py that is able to handle sparse matrices in addition to the standard functionality.

h5py	This is the h5py package, a Python interface to the HDF5 scientific data format.