Searchlight – automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

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.

Researchers at the University of Glasgow 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. The researchers show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). They 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.

Searchlight outline and screenshots

Fig. 1

a Searchlight pipeline schematic. Indicating analysis flow (arrows), text file inputs and outputs (blue boxes), plot outputs (green box), report outputs (red box) and processes (grey boxes). b Screenshot of a Searchlight report, showing plots, the contents side bar and the plot description, legend and R code drop down menus. c Screenshot of the Searchlight Shiny app showing the workflow and plot navigation panel, the plot modification panel and the plot panel

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.

Availability – Project home page:

Cole JJ, Faydaci BA, McGuinness D, Shaw R, Maciewicz RA, Robertson NA, Goodyear CS. (2021) Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. BMC Bioinformatics 22, 411. [article]

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