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.
December 16, 2018: on GitHub and 0.6.16
layersinspired by .loom files allows their information lossless reading via
- initialatization 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 (v0.6.16)
May 1, 2018: version 0.6
- 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
February 9, 2018: version 0.5
- inform about duplicates in
var_namesand resolve them using
- automatically remove unused categories after slicing
.loomfiles using loompy 2
- fixed read/write for a few text file formats
- read UMI tools files:
December 23, 2017: version 0.4
- read/write .loom files
- scalability beyond dataset sizes that fit into memory: see this blog post
rawattribute that simplifies storing the data matrix when you consider it “raw”: see the clustering tutorial