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shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.

To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu.

To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu.

For the detail format of input data, check the Input data format submenu of the Help menu.

Citation

Yu Y+, Yao W+✉, Wang Y, Huang F. shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes. Genomics, Proteomics & Bioinformatics, 2020 (+ co-first author)

Software references

  1. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. R version 3.5.0 (2018)
  2. RStudio and Inc. shiny: Web Application Framework for R. R package version 1.0.5 (2017)
  3. Lionel Henry and Hadley Wickham. rlang: Functions for Base Types and Core R and "Tidyverse" Features. R package version 0.2.1 (2018)
  4. H. Wickham. ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. R package version 3.0.0 (2018)
  5. Gábor Csárdi, Kuba Podgórski, Rich Geldreich. zip: Cross-Platform zip Compression. R package version 2.0.2 (2019)
  6. Erich Neuwirth. RColorBrewer: ColorBrewer palettes. R package version 1.1-2 (2014)
  7. Hadley Wickham. plyr: Tools for Splitting, Applying and Combining Data. R package version 1.8.4 (2016)
  8. Jeffrey B. Arnold. ggthemes: Extra Themes, Scales and Geoms for "ggplot2". R package version 3.4.0 (2017)
  9. Christoph Burow, Urs Tilmann Wolpert and Sebastian Kreutzer. RLumShiny: "Shiny" Applications for the R Package "Luminescence". R package version 0.2.0 (2017)
  10. Baptiste Auguie. gridExtra: Miscellaneous Functions for "Grid" Graphics. R package version 2.3 (2017)
  11. Hadley Wickham. reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package. R package version 1.4.3 (2017)
  12. Matt Dowle and Arun Srinivasan. data.table: Extension of "data.frame". R package version 1.10.4-3 (2017)
  13. JJ Allaire, Jeffrey Horner, Vicent Marti and Natacha Porte. markdown: "Markdown" Rendering for R. R package version 0.8 (2017)

Further references

This application was created by Yiming Yu and Wen Yao. Please send bugs and feature requests to Yiming Yu (yimingyyu at gmail.com) or Wen Yao (venyao at qq.com). This application uses the shiny package from RStudio.

Note

For Mac users, we recommend using shinyChromosome with the Google Chrome browser or other browsers developed based on Chrominum.