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

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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.

rapids-singlecell is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

Installation

New to rapids-singlecell? Check out the installation guide.

Installation
Tutorials

The tutorials walk you through real-world applications of rapids-singlecell.

Tutorials
API reference

The API reference contains a detailed description of the rapids-singlecell API.

API
GitHub

Find a bug? Interested in improving rapids-singlecell? Checkout our GitHub for the latest developments.

https://github.com/scverse/rapids_singlecell

Citation#

If you use rapids-singlecell, please cite:

Dicks, S., et al. (2026). GPU-accelerated single-cell analysis at scale with rapids-singlecell. arXiv. https://doi.org/10.48550/arXiv.2603.02402

News#

  • 30.04.26 v0.15.0 released! This release ships precompiled CUDA kernels via nanobind — no CUDA toolkit needed at install time. Prebuilt wheels for x86_64 and aarch64 support CUDA 12 and 13, covering Turing through Blackwell GPUs. Install with pip install rapids-singlecell-cu13 (or -cu12). See the installation guide for details.

  • 04.03.26 rapids-singlecell is now on arXiv! Check out our preprint: GPU-accelerated single-cell analysis at scale with rapids-singlecell

  • 01.07.25 rapids-singlecell is now an scverse® core package

  • 12.06.25 rapids-singlecell was highlighted in an other NVIDIA technical blog post

  • 07.08.23 rapids-singlecell is now part of scverse® ecosystem.

  • 04.08.23 Thanks to the great team at scverse® rapids-singlecell is now automatically tested with CI

  • 27.06.23 I’m very honored to announce that I was invited to co-author a technical blog post that demonstrates the capabilities and performance of rapids-singlecell for NVIDIA.

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