anndata - Annotated Data

AnnData provides a scalable way of keeping track of data and learned annotations.

• See Scanpy’s documentation for usage related to single cell data.

• Discuss development on GitHub.

• Install via pip install anndata or conda install anndata -c bioconda.

• anndata was initially built for Scanpy (Genome Biology, 2018).

News

COVID-19 datasets distributed as h5ad 2020-04-01

In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s h5ad files: covid19cellatlas.org. It wasn’t anticipated that the initial idea of sharing and backing an on-disk representation of AnnData would become so widely adopted. Curious? Read up more on the format.

Latest additions

On master the future

Bug fixes

• Fixed propagation of import error when importing write_zarr but not all dependencies are installed PR 579 R Hillje

• Fixed issue with .uns sub-dictionaries being referenced by copies PR 576 I Virshup

• Fixed out-of-bounds integer indices not raising IndexError PR 630 M Klein

0.7.6 11 April, 2021

New features

• Added anndata.AnnData.to_memory() for returning an in memory object from a backed one PR 470 PR 542 V Bergen I Virshup

• anndata.AnnData.write_loom() now writes obs_names and var_names using the Index’s .name attribute, if set PR 538 I Virshup

Bug fixes

• Fixed bug where np.str_ column names errored at write time PR 457 I Virshup

• Fixed “value.index does not match parent’s axis 0/1 names” error triggered when a data frame is stored in obsm/varm after obs_names/var_names is updated PR 461 G Eraslan

• Fixed adata.write_csvs when adata is a view PR 462 I Virshup

• Fixed null values being converted to strings when strings are converted to categorical PR 529 I Virshup

• Fixed handling of compression key word arguments PR 536 I Virshup

• Fixed copying a backed AnnData from changing which file the original object points at PR 533 ilia-kats

• Fixed a bug where calling AnnData.concatenate an AnnData with no variables would error PR 537 I Virshup

Deprecations

• Passing positional arguments to anndata.read_loom() besides the path is now deprecated PR 538 I Virshup

• anndata.read_loom() arguments obsm_names and varm_names are now deprecated in favour of obsm_mapping and varm_mapping PR 538 I Virshup

0.7.5 12 November, 2020

Functionality

• Added ipython tab completion and a useful return from .keys to adata.uns PR 415 I Virshup

Bug fixes

• Compatibility with h5py>=3 strings PR 444 I Virshup

• Allow adata.raw = None, as is documented PR 447 I Virshup

• Fix warnings from pandas 1.1 PR 425 I Virshup

0.7.4 10 July, 2020

Concatenation overhaul PR 378 I Virshup

• New function anndata.concat() for concatenating AnnData objects along either observations or variables

• New documentation section: Concatenation

Functionality

• AnnData object created from dataframes with sparse values will have sparse .X PR 395 I Virshup

Bug fixes

• Fixed error from AnnData.concatenate by bumping minimum versions of numpy and pandas issue 385

• Fixed colors being incorrectly changed when AnnData object was subset PR 388

0.7.3 20 May, 2020

Bug fixes

• Fixed bug where graphs used too much memory when copying PR 381 I Virshup

0.7.2 15 May, 2020

Concatenation overhaul I Virshup

• Elements of uns can now be merged, see PR 350

• Outer joins now work for layers and obsm, see PR 352

• Fill value for outer joins can now be specified

• Expect improvments in performance, see issue 303

Functionality

• obsp and varp can now be transposed PR 370 A Wolf

• obs_names_make_unique() is now better at making values unique, and will warn if ambiguities arise PR 345 M Weiden

• obsp is now preferred for storing pairwise relationships between observations. In practice, this means there will be deprecation warnings and reformatting applied to objects which stored connectivities under uns["neighbors"]. Square matrices in uns will no longer be sliced (use .{obs,var}p instead). PR 337 I Virshup

• ImplicitModificationWarning is now exported PR 315 P Angerer

• Better support for ndarray subclasses stored in AnnData objects PR 335 michalk8

Bug fixes

• Fixed inplace modification of Index objects by the make unique function PR 348 I Virshup

• Passing ambiguous keys to obs_vector() and var_vector() now throws errors PR 340 I Virshup

• Fix instantiating AnnData objects from DataFrame PR 316 P Angerer

• Fixed indexing into AnnData objects with arrays like adata[adata[:, gene].X > 0] PR 332 I Virshup

• Fixed type of version PR 315 P Angerer

• Fixed deprecated import from pandas PR 319 P Angerer