RNAseq & Ontology Graphic User Environment

ROGUE (RNA-seq Ontology Graphic User Environment), is an R Shiny application that allows biologists to perform differentially expressed gene analysis, gene ontology and pathway enrichment analysis, potential biomarker identification, and advance statistical analyses.

Notes:

This app was written and tested in R version 3.6.

The below packages are required:

https://www.r-project.org/

Note: This Rshiny app is written to be executed on UNIX and Linux. The application will need to be modified to be executed on Windows.

1. Click on the Code button (top right of file list).

2. Click 'Download ZIP'.

3. Unzip ROGUE-main.zip.

1. tar -zxf [PATH_TO_MAIN_ROGUE_DIRECTORY]/Data/Homo_Sapien.tar.gz --directory [PATH_TO_MAIN_ROGUE_DIRECTORY]/ROGUE-main/Data

   a) Example: (If the folder is in your Home directory's download folder)

    tar -zxf ~/Downloads/ROGUE-main/Data/Homo_Sapien.tar.gz --directory  ~/Downloads/ROGUE-main/Data
   

1. Run the file 'Install_Packages.R'

   a) Rscript [PATH_TO_MAIN_ROGUE_DIRECTORY]/Install_Packages.R

   b) (Alternatively you can load the 'Install_Packages.R' in RStudio and install packages one by one).

    Rscript ~/Downloads/ROGUE-main/Install_Packages.R
   

1. Rscript -e "shiny::runApp('[PATH_TO_MAIN_ROGUE_DIRECTORY]',launch.browser=TRUE)"

   a) Example: (If the folder is in your Home directory's download folder)

   Rscript -e "shiny::runApp('~/Downloads/ROGUE-main',launch.browser=TRUE)"