anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features …

anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features …

Authors: Adam Gayoso, Alex Wolf In this tutorial, we introduce basic properties of the central object, AnnData (“Annotated Data”). AnnData is specifically designed for matrix-like data.

Indexing into an AnnData object can be performed by relative position with numeric indices (like pandas’ iloc()), or by labels (like loc()). To avoid ambiguity with numeric indexing into observations or …

Its attributes are reflected in the Accessors and paths API (anndata.acc). If you want to write e.g. plotting or validation code for anndata objects, look there!

Indexing into an AnnData object can be performed by relative position with numeric indices (like pandas’ iloc()), or by labels (like loc()). To avoid ambiguity with numeric indexing into observations or …

Jan 29, 2026 · Old ways of importing these functions i.e., from anndata import read_csv or from anndata._io.specs import read_elem will still work, but are now considered deprecated and give a …

With concat (), AnnData objects can be combined via a composition of two operations: concatenation and merging. Concatenation is when we keep all sub elements of each object, and stack these …

If 'r', load AnnData in backed mode instead of fully loading it into memory (memory mode). If you want to modify backed attributes of the AnnData object, you need to choose 'r+'.

We anticipate providing async versions of anndata.io.read_elem() and anndata.experimental.read_dispatched() so that users can download data asynchronously without …