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The genotypes of 2058 rice accessions at 8,584,244 SNP sites are stored using Sparse Matrices in R.

Software references

  1. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Short Summer (2017)
  2. RStudio and Inc. shiny: Web Application Framework for R. R package version 1.0.5 (2017)
  3. Eric Bailey. shinyBS: Twitter Bootstrap Components for Shiny. R package version 0.61 (2017)
  4. Paradis E. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419-420. R package version 0.10 (2010)
  5. Shin J-H, Blay S, McNeney B and Graham J. LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms. J Stat Soft, 16 Code Snippet 3. R package version 0.99.4 (2006)
  6. Paradis E., Claude J. & Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290. R package version 5.1 (2004)
  7. Hin-Tak Leung. chopsticks: The snp.matrix and X.snp.matrix classes. R package version 1.42.0 (2015)
  8. H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. R package version 2.2.1 (2009)
  9. D. Kahle and H. Wickham. ggmap: Spatial Visualization with ggplot2. The R Journal, 5(1), 144-161. R package version 2.6.1 (2013)
  10. Hadley Wickham, Romain Francois, Lionel Henry and Kirill Müller. dplyr: A Grammar of Data Manipulation. R package version 0.7.4 (2017)
  11. Hadley Wickham and Lionel Henry. tidyr: Easily Tidy Data with spread() and gather() Functions. R package version 0.8.0 (2017)
  12. Revolution Analytics and Steve Weston. foreach: Provides Foreach Looping Construct for R. R package version 1.4.4 (2015)
  13. Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy. plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.7.1 (2017)
  14. Lawrence M, Huber W, Pag`es H, Aboyoun P, Carlson M, et al. IRanges: Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. R package version 2.12.0 (2013)
  15. Yu G, Smith D, Zhu H, Guan Y and Lam TT. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8, pp. 28-36. R package version 1.10.5 (2016)
  16. Winston Chang. shinythemes: Themes for Shiny. R package version 1.1.1 (2017)
  17. Clayton D. snpStats: SnpMatrix and XSnpMatrix classes and methods. R package version 1.28.0 (2015)
  18. Hadley Wickham. plyr: Tools for Splitting, Applying and Combining Data. R package version 1.8.4 (2016)
  19. Ramnath Vaidyanathan, Yihui Xie, JJ Allaire, Joe Cheng, Kenton Russell, RStudio. htmlwidgets: HTML Widgets for R. R package version 1.3 (2018)

Further references

This application was created by Wen Yao. Please send bugs and feature requests to Wen Yao (venyao at qq.com).