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包装选择和版本管理对单细胞RNA-seq分析的影响

Joseph M Rich^1,2, Lambda Moses¹, Pétur Helgi Einarsson³

¹Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.

bioRxiv : the preprint server for biology

|April 15, 2024

概括

使用Seurat和Scanpy的标准单细胞RNA测序 (scRNA-seq) 分析工作流程,由于潜在的算法变化,产生了显著不同的结果. 用户必须仔细评估这些工具用于可复制scRNA-seq数据分析.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
计算生物学计算生物学

背景情况:

单细胞RNA测序 (scRNA-seq) 是分析细胞异质性的强大技术.
标准的scRNA-seq工作流涉及数据处理,规范化,缩小维度,聚类和微分表达式分析.
塞拉特和Scanpy是用于scRNA-seq分析的占主导地位的软件包,通常被认为可以产生可比结果.

结论:

选择scRNA-seq分析包 (Seurat与Scanpy) 可以显著影响生物学解释.
在生物信息学软件开发中,急需提高透明度,一致性和可重复性.
用户应该批判性地评估他们scRNA-seq分析中使用的工具,以确保可靠的发现.

关键词:

在Scanpy中使用Scanpy.塞拉特·塞拉特是什么意思开源软件是开源的软件.一个单细胞RNA-seqq.

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