anndata - Annotated Data¶
Report issues and see the code on GitHub.
On Master July 29, 2019¶
Breaking changes on master include:
AnnDataobjects don’t have their dimensionality reduced when the main object is subset. This is to maintain consistency when subsetting. See discussion here.
anndata.coremodule currently exists, it may be renamed to
Currently broken features
sc.pp.normalize_per_celldoesn’t work on dask arrays. It just doesn’t modify the matrix.
Views have been overhauled PR #164.
Indexing into a view no longer keeps a reference to intermediate view, issue #62.
Views are now lazy. Elements of view of AnnData are not indexed until they’re accessed.
Indexing with scalars no longer reduces dimensionality of contained arrays, issue #145.
All elements of AnnData should now follow the same rules about how they’re subset, issue #145.
Can now index by observations and variables at the same time.
Post v0.6 June 6, 2019¶
compatibility with Scipy >=1.3 by removing
IndexMixindependency, see here 0.6.20 thanks to P Angerer
bug fix for second-indexing into views, see here 0.6.19 thanks to P Angerer
bug fix for reading excel files 0.6.19 thanks to A Wolf
initialization from pandas DataFrames thanks to A Wolf
support for reading zarr files:
read_zarr()thanks to T White
changed default compression to
write_h5ad()to speed up read and write, disk space use is usually less critical 0.6.16
maintain dtype upon copy 0.6.13 thanks to A Wolf
Version 0.6 May 1, 2018¶
compatibility with Seurat converter
tremendous speedup for
bug fix for deep copy of unstructured annotation after slicing
bug fix for reading HDF5 stored single-category annotations
‘outer join’ concatenation: adds zeros for concatenation of sparse data and nans for dense data
better memory efficiency in loom exports