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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,...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Society of Gastrointestinal Intervention
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769861/ https://www.ncbi.nlm.nih.gov/pubmed/29307145 http://dx.doi.org/10.5808/GI.2017.15.4.178 |
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author | Lee, Tae-Rim Ahn, Jin Mo Kim, Gyuhee Kim, Sangsoo |
author_facet | Lee, Tae-Rim Ahn, Jin Mo Kim, Gyuhee Kim, Sangsoo |
author_sort | Lee, Tae-Rim |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-5769861 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Society of Gastrointestinal Intervention |
record_format | MEDLINE/PubMed |
spelling | pubmed-57698612018-01-19 IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform Lee, Tae-Rim Ahn, Jin Mo Kim, Gyuhee Kim, Sangsoo Genomics Inform Application Note 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. Society of Gastrointestinal Intervention 2017-12 2017-12-29 /pmc/articles/PMC5769861/ /pubmed/29307145 http://dx.doi.org/10.5808/GI.2017.15.4.178 Text en Copyright © 2017 by the Korea Genome Organization It is identical to the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/). |
spellingShingle | Application Note Lee, Tae-Rim Ahn, Jin Mo Kim, Gyuhee Kim, Sangsoo IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform |
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 | Application Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769861/ https://www.ncbi.nlm.nih.gov/pubmed/29307145 http://dx.doi.org/10.5808/GI.2017.15.4.178 |
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