使用ThresholdRq对CITE-seq数据进行自动注销
Mohammad Oliaeimotlagh1, Sunil Kumar2, Aleksandr Taraskin2
1Immunology Center of Georgia, Augusta University, Augusta, GA, USA; Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Cell reports methods
|July 9, 2025
概括
ThresholdR是一款新的R工具,它可以从通过测序 (CITE-seq) 来对转录组和表皮细胞的细胞索引数据中删除噪声. 这种方法通过准确地将信号与噪声分开来改善细胞类型的识别和下游分析.
科学领域:
- 单细胞生物学 单细胞生物学
- 免疫学 免疫学 免疫学
- 生物信息学是一种生物信息学.
背景情况:
- 通过测序 (CITE-seq) 对转录体和表观体的细胞索引集成了转录体和细胞表面蛋白质数据.
- CITE-seq数据 (抗体衍生标签,ADT) 可能包含来自环境抗体的技术噪声,非特异性结合和定位问题.
- 准确的排斥对于可靠地解释CITE-seq实验至关重要.
研究的目的:
- 引入基于R的自动化工具ThresholdR,用于从CITE-seq实验中删除ADT数据.
- 系统地确定每个抗体的信号与噪声分离的值.
- 评估ThresholdR的性能,并与现有方法进行比较.
主要方法:
- 开发一个R套件,ThresholdR,用于自动化ADT数据报销.
- 与DSB和CellBender使用不同的CITE-seq数据集和平台进行基准测试ThresholdR.
- 评估ThresholdR降低虚假负利率的能力.
主要成果:
- 在CITE-seq数据中,ThresholdR有效地识别了ADT的信号噪声值.
- 通过显著降低虚假负率,ThresholdR的表现优于DSB和CellBender.
- 使用ThresholdR的否定方法提高了细胞类型注释的准确性.
结论:
- ThresholdR提供了一种可靠和系统的方法来消除CITE-seq ADT数据.
- 使用ThresholdR去除CITE-seq数据可以改善下游分析,包括细胞类型识别.
- 对于使用CITE-seq技术的研究人员来说,ThresholdR提供了一个有价值的工具.
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