AliGater：一个用于开发大规模、高维细胞计数数据生物信息学管道的框架。
AliGater: a framework for the development of bioinformatic pipelines for large-scale, high-dimensional cytometry data.
作者信息
Ekdahl Ludvig, Arrizabalaga Antton Lamarca, Ali Zain, Cafaro Caterina, de Lapuente Portilla Aitzkoa Lopez, Nilsson Björn
机构信息
Lund Stem Cell Center, Lund University, Lund 221 84, Sweden.
Department of Laboratory Medicine, Lund University, Lund 221 84, Sweden.
出版信息
Bioinform Adv. 2023 Aug 4;3(1):vbad103. doi: 10.1093/bioadv/vbad103. eCollection 2023.
MOTIVATION
AliGater is an open-source framework to accelerate the development of bioinformatic pipelines for the analysis of large-scale, high-dimensional flow cytometry data. AliGater provides a Python package for automatic feature extraction workflows, as well as building blocks to construct analysis pipelines.
RESULTS
We illustrate the use of AliGater in a high-resolution flow cytometry-based genome-wide association study on 46 immune cell populations in 14 288 individuals.
AVAILABILITY AND IMPLEMENTATION
Source code and documentation at https://github.com/LudvigEk/aligater and https://aligater.readthedocs.io.
动机
AliGater是一个开源框架，用于加速生物信息学管道的开发，以分析大规模、高维流式细胞术数据。AliGater提供了一个用于自动特征提取工作流程的Python包，以及构建分析管道的组件。
结果
我们展示了AliGater在一项基于高分辨率流式细胞术的全基因组关联研究中的应用，该研究涉及14288名个体的46个免疫细胞群体。
可用性和实现方式
源代码和文档位于https://github.com/LudvigEk/aligater和https://aligater.readthedocs.io 。
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