https://github.com/scverse/rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
https://github.com/scverse/rapids_singlecell
anndata bioinformatics gpu scverse single-cell
Last synced: 3 months ago
JSON representation
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and 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: 2025-06-30T15:29:56.000Z (11 months ago)
- Last Synced: 2025-06-30T16:24:41.020Z (11 months ago)
- Topics: anndata, bioinformatics, gpu, scverse, single-cell
- Language: Python
- Homepage: https://rapids-singlecell.readthedocs.io/
- Size: 367 MB
- Stars: 216
- Watchers: 9
- Forks: 26
- Open Issues: 20
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-single-cell - RAPIDS-singlecell - [Python] - A GPU-accelerated tool leveraging RAPIDS for scRNA analysis. Seamless scverse compatibility for efficient single-cell data processing and analysis. Replcates features from Scanpy, while also incorporating select functionalities from Squidpy and Decoupler. (Software packages / RNA-seq)
- top-life-sciences - **scverse/rapids_singlecell** - accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.<br>`anndata`, `bioinformatics`, `gpu`, `scverse`, `single-cell`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 96 <img src='https://github.com/HubTou/topgh/blob/main/icons/forks.png'> 18 <img src='https://github.com/HubTou/topgh/blob/main/icons/code.png'> Python <img src='https://github.com/HubTou/topgh/blob/main/icons/license.png'> MIT License <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-06-03 18:07:06 | (Ranked by starred repositories)
README
[](https://github.com/scverse/rapids_singlecell/stargazers)
[](https://pypi.org/project/rapids-singlecell)
[](https://pepy.tech/project/rapids-singlecell)
[](https://rapids-singlecell.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/scverse/rapids_singlecell/actions/workflows/test-gpu.yml)
[](https://codecov.io/gh/scverse/rapids_singlecell)
[](https://scverse.zulipchat.com)
# 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 code, please cite: [](https://zenodo.org/badge/latestdoi/364573913)
Please also consider citing: [rapids-single-cell-examples](https://zenodo.org/badge/latestdoi/265649968) and [scanpy](https://doi.org/10.1186/s13059-017-1382-0)
In addition to that please cite the methods' original research articles in the [scanpy documentation](https://scanpy.readthedocs.io/en/latest/references.html)
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.
