VisualZoneR:一种计算协议,用于识别使用R的单细胞空间转录组的分区区域
Thomas Kerzel1, Stefano Beretta1, Luigi Naldini2
1San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
STAR protocols
|July 27, 2024
概括
本研究介绍了VisualZoneR,这是一种基于R的方法,用于分析空间转录学数据. 它识别出不同的组织区域并测量转录组变化,有助于理解复杂的生物环境.
科学领域:
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
- 计算生物学 计算生物学
背景情况:
- 像Visium和Visium HD这样的空间转录技术可以生成复杂的数据集.
- 分析组织内的隔间区域对于理解生物过程至关重要.
- 现有的方法可能无法完全捕捉空间转录组数据的细微差别.
研究的目的:
- 在单细胞空间转录组学数据中提出一个用于识别单元区区的协议.
- 展示VisualZoneR用于分析组织异质性的应用.
- 为了能够在确定的区域内测量转录组变化.
主要方法:
- 使用VisualZoneR,一个基于R的技术.
- 处理来自Visium或Visium HD的空间转录数据.
- 识别不同的组织区域 (例如,健康的肝脏,转移性区域).
- 整合多个样本并根据边界的近距离分组转录点.
主要成果:
- 在组织样本中成功识别出不同的隔间区域.
- 量化不同区域的转录基因变化.
- 展示VisualZoneR分析空间关系和组织微环境的能力.
结论:
- VisualZoneR提供了一个强大的框架来分析空间转录学数据.
- 该协议有助于识别组织部分和相关的基因表达模式.
- 这种方法增强了对生物组织空间异质性的理解.
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