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 CUDA-X Data Science (formerly 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.
Version-matched agent skill: Released pip packages include an analysis skill for Codex, Claude, and other agents.

Agent skill

Released packages include the matching model-neutral analysis skill:

rapids-singlecell-install-skills --agent codex
rapids-singlecell-install-skills --agent claude
rapids-singlecell-install-skills --agent claude-science  # or: --agent agents
rapids-singlecell-check-kernel                    # before starting Jupyter

Use --dest /path/to/skills/rapids-singlecell for another agent. See the installation guide for installation and preflight details.

Documentation

For more information please have a look through the documentation

Citation

If you use this tool, please cite:

Please cite the relevant tools if used: decoupler for decoupler functions, squidpy for spatial analysis, and pertpy for perturbation analysis.

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.

Metadata

Release files for rapids-singlecell 0.18.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for rapids-singlecell 0.18.1
File	Size	Uploaded
rapids_singlecell-0.18.1.tar.gz	2.4 MB	Oct 12, 2026	Details

Release files / rapids_singlecell-0.18.1.tar.gz

Download URL	rapids_singlecell-0.18.1.tar.gz
Size	2.4 MB
Tags	Source
SHA-256 checksum How to use checksums	`ccf065a45c50ea7afe0be0bd125fe086b82b988ccfa74da817d2f1ebdb078161`
BLAKE2b-256 checksum How to use checksums	`2e9c6543a9d87719288092741e7cbe9f27c3f56328c05850b6f5e9c7763f3fd5`
Upload date	Oct 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/scverse/rapids-singlecell
Publishing commit: github.com/scverse/rapids-singlecell/tree/ad9b8470baf9ee21d9f89ac16e25b43d13115e0a

Workflow

Publishing configuration: github.com/scverse/rapids-singlecell/blob/ad9b8470baf9ee21d9f89ac16e25b43d13115e0a/.github/workflows/publish.yml
Publishing logs: github.com/scverse/rapids-singlecell/actions/runs/38228897969/attempts/1

Artifact

Subject: rapids_singlecell-0.18.1.tar.gz
SHA-256 checksum: ccf065a45c50ea7afe0be0bd125fe086b82b988ccfa74da817d2f1ebdb078161 Verifying attestations