fuhaililab / mdminershiny Goto Github PK

1. Install R on your machine following the instructions on any of these links.
   Windows - https://cran.r-project.org/bin/windows/base/
   Linux - https://cran.r-project.org/doc/manuals/r-release/R-admin.html
   Mac OS X - https://cran.r-project.org/bin/macosx/

2. Download and install the latest version of RStudio
   https://www.rstudio.com/products/rstudio/download2/#download

3. Install Shiny and ShinyDashboard packages by typing the following commands on the R console.
   > install.packages("shiny");
   > install.packages("shinydashboard");

4. Install other dependencies by typing the following commands on the R console.
   > install.packages("RCurl");
   > install.packages("networkD3");
   > install.packages("httr");
   > install.packages("DT");
   > install.packages("igraph");

5. Use Bioconductor as following to install Graphite and Genome annotation packages. Type the following commands in R console.
   > source("https://bioconductor.org/biocLite.R");
   > biocLite();
   > biocLite("graphite”);
   > biocLite("org.Hs.eg.db”);

Click Run App in RStudio. This will open the webapp in a browser.
Click on the Choose File button and upload fold change data of a patient in a .txt file format.
Drug suggestions will be generated in descending order.
Click the desired drug in the table to display drug network, gene network and the merge network.
Click the title of each block to download corresponding data.

#####- Dr. Fuhai Li - Department of Biomedical Informatics, The Ohio State University.

1. Launch a Ubuntu instance on AWS. Follow instruction: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/EC2_GetStarted.html#ec2-launch-instance_linux. When configuring security group, open protocol HTTP and SSH, which opens port 80 and 22 respectively. Set the source of port 22 to your own IP only. Also use Custom TCP RULE to open port 3838 for shiny application.
2. Conncet instance using public key provided by Amazon. For detail instruction: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AccessingInstancesLinux.html
3. Install shiny server on your instance. Follow instruction: https://www.rstudio.com/products/shiny/download-server/
4. Make a directory for your app in /srv/shiny-server. Change the mode of the new folder to 771.
5. Use scp to transfer your shiny project to the new folder you create under /srv/shiny-server.