This repository has been archived and is no longer maintained.
The code is provided for historical reference and may contain unpatched or unknown vulnerabilities.
It should not be used in production systems.






Structure Equation Modeling for In-silico Perturbations (SEMIPs) production version 0.0.2


To run this program locally please do the following:

1) Download and install R (https://www.r-project.org/)

2) Open the *dependencies.R* file and run the script. Please note any errors that may occur during running,
   please make sure to resolve those errors to make sure the dependencies are properly set up.

   If you are running the R 4.x.x, the "parallel" and "tools" have already been installed as base package.

3) Determine the directory of the SignatureAnalysis app on your computer. It will look something like this:

   /Users/li11/myGit/

4) Copy, paste, and run the following line of code in your R command line, using the specific directory of 
   the SignatureAnalysis app on your computer:

   shiny::runApp("/Users/li11/myGit/SEMIPs/")

5) The application should launch and be used interactively

In order to run "Bootstrap", the user needs to firstly run T-scores calculation. The Bootstrap is designed to 
provide "empirical distribution" of elimination with/without replacement through a bootstrap procedure.
Please see the paper "" for details.