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@Zethson Zethson commented Jul 2, 2025

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Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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Zethson added 2 commits July 2, 2025 19:35
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
@Zethson Zethson requested review from kaizhang and Intron7 July 2, 2025 17:52
@PauBadiaM
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Thanks @Zethson!
Could you modify decoupler's description to:

[decoupler](https://github.com/scverse/decoupler) enables the inference of enrichment scores from omics data using prior knowledge.  
It maps omics profiles to annotated biological sets, such as transcription factors, pathways, or kinases, using methods like GSEA, GSVA, and linear models.
Designed for bulk, single-cell and spatial data, decoupler works directly with our scverse core data structures.

Zethson added 2 commits July 3, 2025 09:47
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Intron7 commented Jul 3, 2025

Please write this for RSC:

accelerates the full single-cell analysis pipeline through GPU acceleration with CuPy and NVIDIA RAPIDS. Core steps—including PCA, neighborhood graph construction, and clustering—are executed on GPU using cuML, cuGraph, and custom CUDA/CuPy kernels for peak performance.

RSC integrates directly with AnnData and offers near drop-in replacements not only for scanpy, but also for selected functions from decoupler and squidpy. By preserving familiar APIs and data structures, it enables seamless GPU acceleration of existing workflows—scaling to millions of cells without the computational bottlenecks of CPU-based analysis.

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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