Related Experiment Video
Updated: Dec 20, 2025
14:58
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
4.7K
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data.
Pirunthan Perampalam1,2, Frederick A Dick3,4,5
1London Regional Cancer Program, London Health Sciences Centre, London, ON, N6A 5W9, Canada.
BMC Bioinformatics
|May 31, 2020
Summary
BEAVR is a new browser-based tool simplifying RNA-sequencing (RNA-seq) data analysis and visualization. It empowers researchers without programming knowledge to perform differential gene expression analysis and generate high-quality figures interactively.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- RNA-sequencing (RNA-seq) is widely used in research and clinical settings.
- Existing RNA-seq analysis tools often require programming or Unix/Bash knowledge, creating a barrier for many researchers.
- There is a need for accessible, interactive tools for RNA-seq data analysis and exploration.
Purpose of the Study:
- To introduce BEAVR, a user-friendly, browser-based tool for RNA-sequencing data analysis and visualization.
- To provide researchers, regardless of their programming expertise, with a simplified workflow for exploring RNA-seq data.
- To enable interactive analysis and visualization of differential gene expression (DGE) results.
Main Methods:
- BEAVR is developed in R, utilizing DESeq2 for differential gene expression analysis.
- The tool provides an interactive interface for users with no prior R or DESeq2 knowledge.
- It facilitates obtaining differentially-expressed gene tables, statistical testing, and generating various plots and heatmaps.
Main Results:
- BEAVR enables easy generation of differentially-expressed gene tables with statistical validation.
- Users can interactively visualize RNA-seq results through customizable graphs, plots, and heatmaps.
- The tool allows customization of parameters for statistical testing, variance handling, clustering, and pathway analysis.
Conclusions:
- BEAVR simplifies RNA-seq analysis for novice users and streamlines the process for experts.
- The tool automates several complex analysis steps, enhancing efficiency.
- BEAVR is available on GitHub and as a Docker container for broad accessibility.
Related Concept Videos
03:21RNA-seq
11.6K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.6K
02:24Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K