This is the Shiny application for the paper "The winning methods of predicting cellular position in the DREAM single cell transcriptomics challenge".
To use this Shiny application, you can use RStudio and you will need to install R and Python packages.
We recommend anaconda3 if you need to install python, pip, and conda. You also need to install magic-impute.
In R, you may need to install packages: shiny, shinythemes, reticulate, Rmagic, SCTCwhatateam, and ggplot2. For the SCTCwhatateam, you can install from github https://github.com/thanhbuu04/SCTCwhatateam
In file server.R, you may need to set up the variables below:
c_python <- ".../anaconda3/python.exe"
c_conda <- ".../anaconda3/Scripts/conda.exe"
c_linmethods <- ".../linmethods.py"
c_run_experiment <- ".../runExperiments.R"
c_shiny_run <- ".../Shiny_run" # Folder for output
c_shiny_run_dash <- ".../Shiny_run/shiny_run_" # Output file
In file runExperiments.R, please set the following variable:
c_linmethods_py <- ".../linmethods.py"
c_rlist <- ".../rlist.rda"
The sample data and user guide can be obtained from here: https://github.com/pvvhoang/SCTCwhatateam-ShinyApp/tree/master/Supplementary