Searchlight：使用动态生成的 R 脚本进行自动化批量 RNA-seq 探索和可视化。
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts.
机构信息
Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, Scotland, UK.
GLAZgo Discovery Centre, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, Scotland, UK.
出版信息
BMC Bioinformatics. 2021 Aug 19;22(1):411. doi: 10.1186/s12859-021-04321-2.
BACKGROUND
Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed using R. Though commercial visualisation and interpretation pipelines are comprehensive, freely available pipelines are currently more limited.
RESULTS
Here we demonstrate Searchlight, a freely available bulk RNA-seq visualisation and interpretation pipeline. Searchlight provides: a comprehensive statistical and visual analysis, focusing on the global, pathway and single gene levels; compatibility with most differential experimental designs irrespective of organism or experimental complexity, via three workflows; reports; and support for downstream user modification of plots via user-friendly R-scripts and a Shiny app. We show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). We demonstrate in a timed re-analysis study, that alongside a standard bulk RNA-seq processing pipeline, Searchlight can be used to complete bulk RNA-seq projects up to the point of manuscript quality figures, in under 3 h.
CONCLUSIONS
Compared to a manual R based analysis or current best freely available pipelines (VIPER and BioJupies), Searchlight can reduce the time and effort needed to complete bulk RNA-seq projects to manuscript level. Searchlight is suitable for bioinformaticians, service providers and bench scientists. https://github.com/Searchlight2/Searchlight2 .
背景
一旦批量 RNA-seq 数据经过处理，即比对，然后生成表达和差异表，就需要进行生物学探索、可视化和解释的关键步骤。如果不使用可视化和解释管道，这一步可能会非常耗时且费力，通常使用 R 来完成。尽管商业可视化和解释管道功能全面，但免费提供的管道目前更有限。
结果
在这里，我们展示了免费的批量 RNA-seq 可视化和解释管道 Searchlight。Searchlight 提供了：全面的统计和可视化分析，重点关注全局、途径和单基因水平；通过三个工作流程与大多数差异实验设计兼容，无论生物体或实验复杂性如何；报告；并通过用户友好的 R 脚本和 Shiny 应用程序支持用户对图形进行修改。我们表明，Searchlight 提供了比当前最佳工具（VIPER 和 BioJupies）更高的自动化程度。我们在定时重新分析研究中证明，与标准批量 RNA-seq 处理管道一起，Searchlight 可以在不到 3 小时的时间内完成批量 RNA-seq 项目，直至达到手稿质量的图形。
结论
与手动 R 基础分析或当前最佳免费可用管道（VIPER 和 BioJupies）相比，Searchlight 可以减少完成批量 RNA-seq 项目到手稿水平所需的时间和精力。Searchlight 适用于生物信息学家、服务提供商和基础科学家。https://github.com/Searchlight2/Searchlight2。
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