使用EcoTyper以单细胞分辨率和大规模分析细胞生态系统。
Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper.
作者信息
Steen Chloé B, Luca Bogdan A, Alizadeh Ash A, Gentles Andrew J, Newman Aaron M
机构信息
Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
出版信息
Methods Mol Biol. 2023;2629:43-71. doi: 10.1007/978-1-0716-2986-4_4.
Tissues are composed of diverse cell types and cellular states that organize into distinct ecosystems with specialized functions. EcoTyper is a collection of machine learning tools for the large-scale delineation of cellular ecosystems and their constituent cell states from bulk, single-cell, and spatially resolved gene expression data. In this chapter, we provide a primer on EcoTyper and demonstrate its use for the discovery and recovery of cell states and ecosystems from healthy and diseased tissue specimens.
组织由多种细胞类型和细胞状态组成，这些细胞类型和细胞状态组织成具有特定功能的不同生态系统。EcoTyper是一组机器学习工具，用于从批量、单细胞和空间分辨基因表达数据中大规模描绘细胞生态系统及其组成细胞状态。在本章中，我们提供了EcoTyper的入门介绍，并展示了其在从健康和患病组织样本中发现和恢复细胞状态及生态系统方面的应用。
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