Interactive analysis of single-cell data using flexible workflows with SCTK2.
Interactive analysis of single-cell data using flexible workflows with SCTK2.
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DOI：
10.1016/j.patter.2023.100814
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发表时间：
2023-08-11
期刊：
影响因子：
6.5
通讯作者：
Campbell, Joshua D.
中科院分区：
文献类型：
--
作者：
Wang, Yichen;Sarfraz, Irzam;Pervaiz, Nida;Hong, Rui;Koga, Yusuke;Akavoor, Vidya;Cao, Xinyun;Alabdullatif, Salam;Zaib, Syed Ali;Wang, Zhe;Jansen, Frederick;Yajima, Masanao;Johnson, W. Evan;Campbell, Joshua D.
单细胞RNA测序（scRNA-seq）数据的分析可以揭示复杂生物系统异质性的新见解。已经开发了许多工具和工作流程来执行不同类型的分析。然而，这些工具分布在不同的包或编程环境中，依赖于不同的底层数据结构，并且只能由具有编程语言知识的人使用。在单细胞工具包2（SCTK 2）中，我们集成了各种流行的工具和工作流程，以执行scRNA-seq分析的各个方面。所有工具和工作流程都可以在R控制台中运行，或者使用R/Shiny构建的直观图形用户界面运行。使用Rmarkdown生成的HTML报告可用于记录和概括单个步骤或整个分析工作流程。我们表明，与现有工具相比，该工具包提供了更多的功能，并允许非计算用户无缝分析scRNA-seq数据。包括直观的图形用户界面，用于scRNA-seq数据的交互式分析允许非计算用户通过端到端工作流程分析scRNA-seq数据提供跨不同编程环境的工具之间的互操作性生成HTML报告，以实现重现性和轻松共享结果单细胞数据可用于了解复杂的生物系统。然而，许多单细胞分析工具只能由训练有素的计算生物学家使用，并且分散在不同的编程语言中。单细胞工具包（SCTK）是一个软件包，它将许多不同的工具集中在一个地方，并允许非计算用户使用图形用户界面分析自己的数据。总的来说，SCTK使计算和非计算研究人员能够访问各种各样的单细胞工具来执行复杂的分析工作流程。单细胞工具包（SCTK）是一个软件包，使计算和非计算研究人员能够利用各种工具和复杂的工作流程进行单细胞分析。
Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity of complex biological systems. Many tools and workflows have been developed to perform different types of analyses. However, these tools are spread across different packages or programming environments, rely on different underlying data structures, and can only be utilized by people with knowledge of programming languages. In the Single-Cell Toolkit 2 (SCTK2), we have integrated a variety of popular tools and workflows to perform various aspects of scRNA-seq analysis. All tools and workflows can be run in the R console or using an intuitive graphical user interface built with R/Shiny. HTML reports generated with Rmarkdown can be used to document and recapitulate individual steps or entire analysis workflows. We show that the toolkit offers more features when compared with existing tools and allows for a seamless analysis of scRNA-seq data for non-computational users. Includes an intuitive graphical user interface for interactive analysis of scRNA-seq data Allows non-computational users to analyze scRNA-seq data with end-to-end workflows Provides interoperability between tools across different programming environments Produces HTML reports for reproducibility and easy sharing of results Single-cell data can be used to understand complex biological systems. However, many single-cell analysis tools can only be used by trained computational biologists and are scattered across different programming languages. The Single-Cell Toolkit (SCTK) is a software package that brings together many different tools in one place and allows non-computational users to analyze their own data using a graphical user interface. Overall, SCTK gives computational and non-computational researchers the ability to access a wide variety of single-cell tools to perform complex analysis workflows. The Single Cell Toolkit (SCTK) is a software package that gives computational and non-computational researchers the ability to utilize a wide variety of tools and complex workflows for single-cell analysis.
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影响因子：
16.6
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Hong R;Koga Y;Bandyadka S;Leshchyk A;Wang Y;Akavoor V;Cao X;Sarfraz I;Wang Z;Alabdullatif S;Jansen F;Yajima M;Johnson WE;Campbell JD
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