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:
shiny | shinydashboard | shinyWidgets | shinyjs | markdown |
edgeR | MASS | pheatmap | plotly | heatmaply |
RColorBrewer | ggplot2 | dplyr | Rtsne | scatterplot3d |
gridExtra | gtools | colourpicker | grid | cowplot |
fgsea | reshape2 | rintrojs | DESeq2 | uwot |
shinyalert | shinycssloaders |
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.
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Click on the Code button (top right of file list).
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Click 'Download ZIP'.
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Unzip ROGUE-main.zip.
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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
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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
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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)"