anndata - Annotated Data¶
pip install anndata or
conda install anndata -c bioconda.
Report issues and see the code on GitHub.
AnnData provides a scalable way of keeping track
of data together with learned annotations. It is used within Scanpy, for which it was initially
developed. Both packages have been introduced in Genome Biology (2018).
See all releases here. The following lists selected improvements.
On master March 23, 2019¶
- maintain dtype upon read/write to appear as 0.7
- bug fix for https://github.com/theislab/anndata/issues/126 0.6.19
- bug fix for reading excel files 0.6.19
layersinspired by .loom files allows their information lossless reading via
- initialization from pandas DataFrames
- iteration over chunks
- support for reading zarr files:
- 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
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