TOmicsVis: An all‐in‐one transcriptomic analysis and visualization R package with Shinyapp interface

Abstract

Abstract Transcriptomic analysis has been widely used in comparative experiments to uncover biological mechanisms in various species. However, a simple tool is still lacking to optimize and integrate the features from multiple R packages. In this study, we developed TOmicsVis (Transcriptomics Visualization) (CRAN: https://cran.r-project.org/package=TOmicsVis, v2.0.0), an R package that provides a comprehensive solution for transcriptomics analysis and visualization. It utilizes 46 R packages to design 40 suitable functions for the streamlined analysis of multigroup transcriptomic projects, which covers six main categories: Sample Statistics, Traits Analysis, Differential Expression, Advanced Analysis, GO and KEGG Enrichment, and Table Operation. TOmicsVis can be performed either locally or online (https://shiny.hiplot.cn/tomicsvis-shiny/), which provides significant convenience for researchers without coding training. These user‐friendly visualization functions and built‐in analysis capabilities enable researchers to monitor experimental data dynamics promptly and explore transcriptomics data quickly.

Keywords

• data visualization
• differential expression
• enrichment analysis
• multigroup RNA‐Seq
• shinyapp