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Article
BEAVR: A browser-based tool for the exploration and visualization of RNA-seq data
BMC Bioinformatics
  • Pirunthan Perampalam, London Regional Cancer Program
  • Frederick A. Dick, London Regional Cancer Program
Document Type
Article
Publication Date
5-29-2020
URL with Digital Object Identifier
10.1186/s12859-020-03549-8
Abstract

Background: The use of RNA-sequencing (RNA-seq) in molecular biology research and clinical settings has increased significantly over the past decade. Despite its widespread adoption, there is a lack of simple and interactive tools to analyze and explore RNA-seq data. Many established tools require programming or Unix/Bash knowledge to analyze and visualize results. This requirement presents a significant barrier for many researchers to efficiently analyze and present RNA-seq data. Results: Here we present BEAVR, a Browser-based tool for the Exploration And Visualization of RNA-seq data. BEAVR is an easy-to-use tool that facilitates interactive analysis and exploration of RNA-seq data. BEAVR is developed in R and uses DESeq2 as its engine for differential gene expression (DGE) analysis, but assumes users have no prior knowledge of R or DESeq2. BEAVR allows researchers to easily obtain a table of differentially-expressed genes with statistical testing and then visualize the results in a series of graphs, plots and heatmaps. Users are able to customize many parameters for statistical testing, dealing with variance, clustering methods and pathway analysis to generate high quality figures. Conclusion: BEAVR simplifies analysis for novice users but also streamlines the RNA-seq analysis process for experts by automating several steps. BEAVR and its documentation can be found on GitHub at https://github.com/developerpiru/BEAVR. BEAVR is available as a Docker container at https://hub.docker.com/r/pirunthan/beavr.

Citation Information
Pirunthan Perampalam and Frederick A. Dick. "BEAVR: A browser-based tool for the exploration and visualization of RNA-seq data" BMC Bioinformatics Vol. 21 Iss. 1 (2020)
Available at: http://works.bepress.com/frederick-dick/9/