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,...
Saved in:
| Main Authors: | , , , |
|---|---|
| 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 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832572690101174272 |
|---|---|
| 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. |
| format | Article |
| id | doaj-art-72c4fb9eae7e498dad416b1695aa55b5 |
| 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 |
| work_keys_str_mv | AT taerimlee ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform AT jinmoahn ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform AT gyuheekim ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform AT sangsookim ivaganintegrativevisualizationapplicationforvarioustypesofgenomicdatabasedonrshinyandthedockerplatform |