DEploid-ShinyApp is an interactive web interface for DEploid (also available in R). DEploid is designed for deconvoluting mixed genomes with unknown proportions. DEploid-ShinyApp provides a user friendly interface to interact the deconvoluted haplotypes with specific population groups, and look up for existing drug resistance mutations and etc.
Make sure you have the following R packages installed.
install.packages(c("shinythemes", "shinyjs", "shiny", "dplyr", "quantmod",
"RCurl", "plotly", "ggplot2", "dygraphs", "DEploid", "leaflet", "stringr"))Download DEploid-ShinyApp from the git repository,
$ git clone git@github.com:shajoezhu/DEploid-ShinyApp.git
$ cd DEploid-ShinyApplaunch R under the DEploid-ShinyApp directory and type the following:
shiny::runApp()DEploid-ShinyApp require user to provide a VCF file. Assume all variants are PASS in the QUAL column, the VCF file also reqires the AD field. In the current implementation, DEploid-ShinyApp only take the first sample in the VCF file. DEploid-ShinyApp DO NOT handle multi-allelic variants, nor indels. The FILTER column will not be used.
You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.
If you use dEploid in your work, please cite the program:
Zhu, J. S. J. Almagro-Garcia G. McVean. (2017) Deconvoluting multiple infections in Plasmodium falciparum from high throughput sequencing data. bioRxiv 099499. doi: https://doi.org/10.1101/099499