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anndata - Annotated Data

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Report issues and see the code on GitHub.

AnnData provides a scalable way of keeping track of data and learned annotations. It was initially built for Scanpy (Genome Biology, 2018).

Latest release

On master

Upcoming changes

0.7.3 2020-05-20

Bug fixes

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

0.7.2 2020-05-15

Concatenation overhaul I Virshup

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

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

  • Fill value for outer joins can now be specified

  • Expect improvments in performance, see #303

Functionality

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

  • obs_names_make_unique() is now better at making values unique, and will warn if ambiguities arise #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). #337 I Virshup

  • ImplicitModificationWarning is now exported #315 P Angerer

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

Bug fixes

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

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

  • Fix instantiating AnnData objects from DataFrame #316 P Angerer

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

  • Fixed type of version #315 P Angerer

  • Fixed deprecated import from pandas #319 P Angerer