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scientific-gpu-singlecell

Run GPU-accelerated single-cell preprocessing, PCA, clustering, and embedding on AnnData objects.

3|1|Updated Feb 11, 2026
Search Tags:#gpu#single-cell#clustering#anndata#rapids#cuml#cugraph
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-gpu-singlecell
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-gpu-singlecell
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-gpu-singlecell
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-gpu-singlecell

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

The GPU-accelerated single-cell analysis pipeline reduces the time and resources required to process and analyze very large single-cell datasets by leveraging GPU acceleration.

Core Features & Use Cases

  • GPU-accelerated preprocessing, QC, HVG selection, and scaling on large datasets
  • GPU-based PCA/kNN, Leiden/Louvain clustering, and GPU embeddings (UMAP/t-SNE)
  • Designed for large-scale (>1M cells), multi-sample integration, and benchmarking scenarios

Quick Start

Run the GPU-accelerated single-cell pipeline on your AnnData object to perform pre-processing, PCA, clustering, and embedding.

Frequently Asked Questions about scientific-gpu-singlecell

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run single-cell clustering and UMAP on datasets with over a million cells?▼

You can use GPU-accelerated single-cell analysis to process million-cell datasets. It performs preprocessing, PCA, Leiden clustering, and UMAP on GPUs using RAPIDS libraries like cuML and cuGraph.

Do I need RAPIDS libraries to run GPU-accelerated single-cell analysis?▼

Yes, GPU-accelerated single-cell analysis requires RAPIDS libraries (cuML/cuGraph) for PCA, kNN, and clustering. It integrates with AnnData-compatible workflows to enable seamless GPU pipelines.

Can I use AnnData objects with a GPU-based single-cell pipeline?▼

Yes, GPU-accelerated single-cell analysis supports AnnData-compatible workflows. It enables seamless GPU-accelerated pipelines for preprocessing, HVG selection, PCA, and clustering on your existing objects.

What is the best way to perform multi-sample integration for large-scale single-cell data?▼

GPU-accelerated single-cell analysis is designed for large-scale multi-sample integration. It leverages GPUs to handle preprocessing, clustering, and embeddings for datasets exceeding one million cells.

Does GPU-accelerated single-cell analysis support Leiden and Louvain clustering?▼

Yes, GPU-accelerated single-cell analysis supports GPU-based Leiden and Louvain clustering. It uses RAPIDS cuGraph to perform these clustering methods efficiently on large-scale datasets.

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