anndata - Annotated Data¶
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).
On Master July 29, 2019¶
Warning
Breaking changes on master include:
Elements of
AnnData
objects don’t have their dimensionality reduced when the main object is subset. This is to maintain consistency when subsetting. See discussion here.While the
anndata.core
module currently exists, it may be renamed toanndata._core
#174.
Currently broken features
sc.pp.normalize_per_cell
doesn’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¶
convenience accesors
obs_vector()
,var_vector()
for 1d arrays, see here 0.6.21 thanks to I Virshupcompatibility with Scipy >=1.3 by removing
IndexMixin
dependency, see here 0.6.20 thanks to P Angererbug 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
layers
inspired by .loom files allows their information lossless reading viaread_loom()
thanks to S Rybakovinitialization from pandas DataFrames thanks to A Wolf
iteration over chunks
chunked_X()
andchunk_X()
thanks to S Rybakovsupport for reading zarr files:
read_zarr()
thanks to T Whitechanged default compression to
None
inwrite_h5ad()
to speed up read and write, disk space use is usually less critical 0.6.16maintain dtype upon copy 0.6.13 thanks to A Wolf
Version 0.6 May 1, 2018¶
compatibility with Seurat converter
tremendous speedup for
concatenate()
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
Version 0.5 February 9, 2018¶
inform about duplicates in
var_names
and resolve them usingvar_names_make_unique()
automatically remove unused categories after slicing
read/write
.loom
files using loompy 2fixed read/write for a few text file formats
read UMI tools files:
read_umi_tools()