scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis
复制标题
DOI：
10.1093/bioinformatics/btz830
复制
发表时间：
2020-03-15
期刊：
影响因子：
5.8
通讯作者：
Cai, James J.
中科院分区：
文献类型：
--
作者：
Cai, James J.
动机：单细胞RNA测序(scRNA-seq)技术彻底改变了生物医学科学的研究方式。它为研究细胞异质性和基因表达可变性提供了前所未有的跨单个细胞的分辨率水平。然而，由于scRNA-seq数据的稀疏性和高维性，分析scRNA-seq数据是一项具有挑战性的工作。它包含一套全面的功能，用于数据归一化、特征选择、批量校正、归责、细胞聚类、轨迹/伪时间分析和网络构建，这些功能可以组合和集成来构建定制工作流。尽管大多数函数都是在原生的MatLab中实现的，但提供的包装函数允许用户调用用MatLab或其他语言开发的“第三方”工具。此外，scGEAToolbox配备了由App Designer生成的复杂图形用户界面，使其成为易于使用的快速数据处理应用程序。
Motivation: Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way research is done in biomedical sciences. It provides an unprecedented level of resolution across individual cells for studying cell heterogeneity and gene expression variability. Analyzing scRNA-seq data is challenging though, due to the sparsity and high dimensionality of the data.Results: I developed scGEAToolbox-a Matlab toolbox for scRNA-seq data analysis. It contains a comprehensive set of functions for data normalization, feature selection, batch correction, imputation, cell clustering, trajectory/pseudotime analysis and network construction, which can be combined and integrated to building custom workflow. Although most of the functions are implemented in native Matlab, wrapper functions are provided to allow users to call the 'third-party' tools developed in Matlab or other languages. Furthermore, scGEAToolbox is equipped with sophisticated graphical user interfaces generated with App Designer, making it an easy-to-use application for quick data processing.