anndata: Access and store annotated datamatrices
Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf
Abstract
anndata is a Python package for handling annotated data matrices in memory and on disk (github.com/scverse/anndata),positioned between pandas and xarray.anndata offers generic data access features including, among others, sparse data support, lazy operations, and a PyTorch interface. Statement of needGenerating insight from high-dimensional data matrices typically works through training models that annotate observations and variables via low-dimensional representations.In exploratory data analysis, this involves iterative training and analysis using original and learned annotations and task-associated representations.anndata offers a canonical data structure for book-keeping these, which is neither addressed by pandas (McKinney, 2010), nor xarray (Hoyer & Hamman, 2017), nor commonly-used modeling packages like scikit-learn (Pedregosa et al., 2011).