Tools

• shinyCircos V2: updating shinyCircos with more advanced features
  • Source code: https://github.com/YaoLab-Bioinfo/shinyCircos-V2.0
  • Online use: https://venyao.xyz/shinyCircos/
  • Online use: https://asiawang.shinyapps.io/shinyCircos/
    
• shinyCircos: an R/Shiny application for interactive creation of Circos plot
  • Source code: https://github.com/YaoLab-Bioinfo/shinyCircos
  • Online use: https://venyao.xyz/shinyCircos-V1/
  • Online use: https://yimingyu.shinyapps.io/shinycircos/
    
  • Online use: https://venyao.shinyapps.io/shinyCircos/
• shinyChromosome: an R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes
  • Source code: https://github.com/venyao/shinyChromosome
  • Online use: https://venyao.xyz/shinyChromosome
  • Online use: https://yimingyu.shinyapps.io/shinychromosome
    
  • Online use: https://venyao.shinyapps.io/shinyChromosome/
    
• ECOGEMS: a comprehensive SNP database with 8,584,244 SNP sites among 2058 rice accessions
  • Source code: https://github.com/venyao/ECOGEMS
    
  • Online use: https://venyao.xyz/ECOGEMS/
• funRiceGenes: a comprehensive database of functionally characterized rice genes
  • Online use: https://funricegenes.github.io/
  • Online use: https://venyao.xyz/funRiceGenes/
    
• binQTL: an R package for mapping QTL using Binned Genotypes
  • Source code: https://github.com/venyao/binQTL
  • Source code: https://github.com/venyao/binQTL.shiny
  • Online use: https://venyao.xyz/binQTL.shiny/
    
  • Online use: https://venyao.shinyapps.io/binQTL/
    
• MaizeSNPDB: a comprehensive SNP database of 1210 maize lines
  • Source code: https://github.com/venyao/MaizeSNPDB
  • Online use: https://venyao.xyz/MaizeSNPDB/
    
• intansv: an R package for integrative analysis of structural variations
  • Web site: https://venyao.github.io/intansv/
  • Source code: https://github.com/venyao/intansv
  • Source code: http://www.bioconductor.org/packages/release/bioc/html/intansv.html
  • Source code: http://www.bioconductor.org/packages/devel/bioc/html/intansv.html
• LIRBase: a comprehensive collection of long inverted repeats in 427 eukaryotes
  • Source code: https://github.com/venyao/LIRBase
  • Online use: https://venyao.xyz/lirbase/
    
• SoybeanGDB: a comprehensive genome database of soybean
  • Source code: https://github.com/venyao/SoybeanGDB
  • Online use: https://venyao.xyz/soybeangdb/