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

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,...

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Main Authors: Tae-Rim Lee, Jin Mo Ahn, Gyuhee Kim, Sangsoo Kim
Format: Article
Language:English
Published: BioMed Central 2017-12-01
Series:Genomics & Informatics
Subjects:
Online Access:http://genominfo.org/upload/pdf/gi-2017-15-4-178.pdf
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author Tae-Rim Lee
Jin Mo Ahn
Gyuhee Kim
Sangsoo Kim
author_facet Tae-Rim Lee
Jin Mo Ahn
Gyuhee Kim
Sangsoo Kim
author_sort Tae-Rim Lee
collection DOAJ
description 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.
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institution Kabale University
issn 2234-0742
language English
publishDate 2017-12-01
publisher BioMed Central
record_format Article
series Genomics & Informatics
spelling doaj-art-72c4fb9eae7e498dad416b1695aa55b52025-02-02T08:39:17ZengBioMed CentralGenomics & Informatics2234-07422017-12-0115417818210.5808/GI.2017.15.4.178502IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker PlatformTae-Rim LeeJin Mo AhnGyuhee KimSangsoo KimNext-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.http://genominfo.org/upload/pdf/gi-2017-15-4-178.pdfdockergenome browsergenome-wide association studyRNA sequencingShinyvisualization
spellingShingle Tae-Rim Lee
Jin Mo Ahn
Gyuhee Kim
Sangsoo Kim
IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
Genomics & Informatics
docker
genome browser
genome-wide association study
RNA sequencing
Shiny
visualization
title IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
title_full IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
title_fullStr IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
title_full_unstemmed IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
title_short IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform
title_sort ivag an integrative visualization application for various types of genomic data based on r shiny and the docker platform
topic docker
genome browser
genome-wide association study
RNA sequencing
Shiny
visualization
url http://genominfo.org/upload/pdf/gi-2017-15-4-178.pdf
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AT gyuheekim ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform
AT sangsookim ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform