Dependencies

For successful implementation of the software, please make sure that your system has following:

• Software

  • Bedtools: The tool assumes bedtools in the path. Else You can download the latest version of the bedtools from page: https://code.google.com/p/bedtools/downloads/list. After installation, please make sure bedtools is in the path.

• Python modules:

  • Scipy: visit http://www.scipy.org/install.html
  • Matplotlib: visit http://matplotlib.org/users/installing.html
  • Numpy: visit http://docs.scipy.org/doc/numpy/user/install.html
  • scikit-learn: visit http://scikit-learn.org/stable/install.html

• Perl modules:

  • CWD: visit http://search.cpan.org/~rjbs/PathTools-3.59/Cwd.pm
  • Math::Round visit http://search.cpan.org/dist/Math-Round/Round.pm
  • Install them from CPAN shell: http://www.twiki.org/cgi-bin/view/TWiki/HowToInstallCpanModules

• R library:

  • GenomicRanges: visit https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

Installation

1. GitHub:

   Run in terminal: git clone https://github.com/ajinkya-deogade/GEP.git

2. Download from https://github.com/ajinkya-deogade/GEP/archive/master.zip

   Download it and uncompressed the code as: gzip GEP-master.zip