https://github.com/scverse/rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis
https://github.com/scverse/rapids-singlecell

anndata bioinformatics gpu scverse single-cell

Last synced: 2 months ago
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rapids-singlecell: GPU-accelerated framework for scRNA analysis

• Host: GitHub
• URL: https://github.com/scverse/rapids-singlecell
• Owner: scverse
• License: mit
• Created: 2021-05-05T12:46:51.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2026-03-24T05:17:57.000Z (2 months ago)
• Last Synced: 2026-03-29T15:19:29.030Z (2 months ago)
• Topics: anndata, bioinformatics, gpu, scverse, single-cell
• Language: Python
• Homepage: https://rapids-singlecell.readthedocs.io/
• Size: 368 MB
• Stars: 341
• Watchers: 7
• Forks: 43
• Open Issues: 22
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing.md
  • License: LICENSE

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# rapids-singlecell: GPU-Accelerated Single-Cell Analysis within scverse®

rapids-singlecell provides GPU-accelerated single-cell analysis with an AnnData-first API.

It is largely compatible with Scanpy and includes selected functionality from Squidpy, decoupler, and pertpy.

Computations use CuPy and NVIDIA RAPIDS for performance on large datasets.

- **GPU acceleration**: Common single-cell workflows on `AnnData` run on the GPU.

- **Ecosystem compatibility**: Works with Scanpy APIs; includes pieces from Squidpy, decoupler, and pertpy.

- **Simple installation**: Available via Conda and PyPI.

## Documentation

For more information please have a look through the [documentation](https://rapids-singlecell.readthedocs.io/en/latest/)

## Citation

If you use this tool, please cite: [![arXiv](https://img.shields.io/badge/arXiv-2603.02402-b31b1b.svg)](https://doi.org/10.48550/arXiv.2603.02402)

Please cite the relevant tools if used: [decoupler](https://doi.org/10.1093/bioadv/vbac016) for decoupler functions, [squidpy](https://doi.org/10.1038/s41592-021-01358-2) for spatial analysis, and [pertpy](https://doi.org/10.1038/s41592-024-02233-6) for perturbation analysis.

[//]: # (numfocus-fiscal-sponsor-attribution)

rapids-singlecell is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.