shinyChromosome:An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes
- Author:
Yu YIMING
1
;
Yao WEN
;
Wang YUPING
;
Huang FANGFANG
Author Information
1. National Key Laboratory of Wheat and Maize Crop Science
- Keywords:
Genomic data visualization;
Non-circular whole genome plot;
Shiny application;
Graphical user interface;
shinyChromosome
- From:
Genomics, Proteomics & Bioinformatics
2019;17(5):535-539
- CountryChina
- Language:Chinese
-
Abstract:
Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce non-circular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require improvement, including the addition of new functionalities. To address these issues, we developed a new R/Shiny application, named shinyChromosome, as a GUI for the interactive creation of non-circular whole genome diagrams. shinyChromosome can be easily installed on personal computers for own use as well as on local or public servers for community use. Publication-quality images can be readily generated and anno-tated from user input using diverse widgets. shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.
