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anndata - Annotated Data

Install via 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

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

Version 0.4 December 23, 2017

  • read/write .loom files
  • scalability beyond dataset sizes that fit into memory: see this
    blog post
  • AnnData has a raw attribute
    that simplifies storing the data matrix when you consider it “raw”: see the clustering tutorial