{"categories":[{"label":"Visualization","url":"https://skillfed.io/packages/category/scientific-engineering-visualization"},{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"}],"enrichment":{"capability":"anndata handles annotated data matrices in memory and on disk with sparse data support, lazy operations, and efficient storage\u2014positioned as a middle ground between pandas and xarray for scientific data.","skillfed_tags":["bioinformatics","sparse-matrices","data-containers"],"use_cases":["Store and manipulate single-cell RNA-seq data with cell metadata and gene annotations.","Work with large sparse matrices that don't fit efficiently in pandas or numpy alone.","Persist annotated datasets to disk in HDF5 or Zarr format for reproducible analysis.","Build data pipelines that combine in-memory and disk-backed operations with lazy loading.","Integrate with Scanpy or other scverse tools for downstream bioinformatics workflows."],"what_it_does":"anndata is a Python library for storing and manipulating annotated data matrices\u2014arrays with associated metadata, observations, and variables. It sits between pandas DataFrames and xarray Datasets, designed to handle scientific data efficiently whether in memory or on disk. The package supports sparse matrices, lazy operations, and multiple storage backends including HDF5 and Zarr, making it suitable for datasets that range from small in-memory arrays to larger disk-backed collections.\n\nThe library was originally built for Scanpy, a single-cell analysis toolkit, but has become a general-purpose container for annotated matrices across bioinformatics and other scientific domains. It depends on numpy, pandas, scipy, h5py, zarr, and several utility packages, giving it a stable foundation in the scientific Python ecosystem. The package is actively maintained as part of the scverse project and fiscally sponsored by NumFOCUS.","worth_installing":"Yes. anndata is actively maintained, has no known vulnerabilities, low install friction, and fills a genuine need for annotated matrix storage in scientific Python. Its BSD-3-Clause permissive license poses no restriction. Install it if you work with structured scientific data\u2014especially single-cell omics\u2014or need sparse matrix support with metadata. The Python 3.12 or later requirement is a minor constraint for modern projects."},"id":"anndata","links":{"html":"https://skillfed.io/packages/anndata","md":"https://skillfed.io/packages/anndata.md","pypi":"https://pypi.org/project/anndata/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2026-07-13","license_spdx":"BSD-3-Clause","license_treatment":"permissive","name":"anndata","python_support":"supports_current","summary":"Annotated data."},"popularity":{"monthly_downloads":1812748,"position":3528,"tier":"top_5000"},"security":{"n_vulnerabilities":0},"version":"0.13.2"}