构建标准化单细胞数据集scUnified,助力算法公平对比与复现
scUnified: An AI-Ready Standardized Resource for Single-Cell RNA Sequencing Analysis
- 整合13个高质量单细胞数据集,统一格式与预处理流程
- 覆盖人鼠两物种、九类组织,支持直接用于算法测试
- 为细胞聚类等任务提供可复现的基准评估平台
单细胞RNA测序技术能系统揭示细胞状态与相互作用,为理解细胞异质性提供关键信息。基于此,已有大量计算方法被用于细胞聚类、细胞类型注释和标志基因识别等任务。为全面评估和比较这些方法,标准化、分析就绪的数据集至关重要。然而,此类数据集仍稀缺,且数据格式、预处理流程与注释策略的差异严重阻碍了可复现性,并增加了现有方法系统评估的难度。为此,我们提出scUnified——一个面向人工智能的标准化单细胞RNA测序资源,整合了13个高质量数据集,涵盖人和小鼠两个物种及九种组织类型。所有数据均经过统一的质量控制与预处理,以一致格式存储,可直接用于各类计算分析而无需额外清洗。我们进一步通过代表性生物任务的实验分析展示了scUnified的实用性,为在统一数据集上标准化评估计算方法提供了可复现的基础。
原文摘要 · Abstract (English)
Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have been developed for tasks such as cell clustering, cell type annotation, and marker gene identification. To fully assess and compare these methods, standardized, analysis-ready datasets are essential. However, such datasets remain scarce, and variations in data formats, preprocessing workflows, and annotation strategies hinder reproducibility and complicate systematic evaluation of existing methods. To address these challenges, we present scUnified, an AI-ready standardized resource for single-cell RNA sequencing data that consolidates 13 high-quality datasets spanning two species (human and mouse) and nine tissue types. All datasets undergo standardized quality control and preprocessing and are stored in a uniform format to enable direct application in diverse computational analyses without additional data cleaning. We further demonstrate the utility of scUnified through experimental analyses of representative biological tasks, providing a reproducible foundation for the standardized evaluation of computational methods on a unified dataset.
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