Genomics Inform.  2017 Dec;15(4):178-182. 10.5808/GI.2017.15.4.178.

IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform

• Lee TR
• Ahn JM
• Kim G
• Kim S

• KMID: 2404056
• DOI: http://doi.org/10.5808/GI.2017.15.4.178

Abstract

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

Keyword

docker; genome browser; genome-wide association study; RNA sequencing; Shiny; visualization

MeSH Terms

Dataset
Genome
Genome-Wide Association Study
Genomics
Humans
Linkage Disequilibrium
Sequence Analysis, RNA