System setup

Requirements

The secomo package is compatible and was tested with py2.7, py3.4, py3.5 and py3.5. Prerequisites:

  • theano
  • numpy
  • scipy
  • joblib
  • Biopython
  • matplotlib
  • pandas
  • weblogolib
  • scikit-learn
  • seaborn

The latter collection of packages are necessary to investigate the model results using our set of provided functions (e.g. secomo.utils.scatterTSNE()).

Finally, if possible, we recommend utilizing CUDA. Theano take advantage of cuda, which significantly speeds up the training phase. See Theano documention for more information.

Installation

The secomo package can be obtained from GitHub

At the moment you can install it according to:

git clone https://github.com/schulter/crbm.git
cd crbm/
python setup.py install