anndata: Access and store annotated datamatrices
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).
Authors
- Isaac Virshup (ORCID: https://orcid.org/0000-0002-1710-8945)
- Philipp Angerer (ORCID: https://orcid.org/0000-0002-0369-2888)
- F. Alexander Wolf (ORCID: https://orcid.org/0000-0002-8760-7838)
- Fabian Joachim Theis (ORCID: https://orcid.org/0000-0002-2419-1943)
- Sergei Rybakov (ORCID: https://orcid.org/0000-0002-4944-6586)
Publication Details
- Journal
- The Journal of Open Source Software
- Published
- 2024-09-16
- DOI
- https://doi.org/10.21105/joss.04371
- Citations
- 164
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 38.35