Emig Reimplementation

OVERVIEW

This is a tool for target prioritization that reimplements the approach taken in Emig et al. (2013).

The user can set up the options to run the tool using the configuration file. More details can be found under README_CONFIGURATION.txt file.

HARDWARE REQUIREMENTS

The hardware requirements to run the program are:

1. At least 8GB of RAM

SOFTWARE REQUIREMENTS

The software requirements to run the program are:

1. Ubuntu (>=16.04). You can try other OS, but they are not supported
2. Python (>=3.5)
3. R (>=3.3.3)
4. All Python libraries specified under requirements.txt
5. All R packages specified under DESCRIPTION

INPUT FILES

There are 4 files which are necessary to run this program:

1. A protein-protein interaction network in the format of:

   EntrezID EntrezID CONFIDENCE

   Such as:

   216 216 0.76

   3679 1134 0.73

   55607 71 0.65

   5552 960 0.63

   2886 2064 0.9

   5058 2064 0.73

   1742 2064 0.87

   An example of such a network can be found [here](http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/download.php)

2. An experiment file, in Excel format. Rows show individual entries, columns are the values of the following properties:

   • Log fold change
   • Adjusted p value
   • Entrez id

   The file may contain other columns too, but the indices and names of the above columns must be entered to the configuration file.

3. A list of Entrez ids of known targets, in the format of

   EntrezID1

   EntrezID2

   ...

   Such as:

   1742

   3996

   150

   152

   151

4. A configuration file. The path to the file is input at the beginning of the program. Details can be found under README_CONFIGURATION.md

HOW TO RUN