Installation

Installation and Data

Prerequisites:

• python
• numpy and scipy
• matplotlib
• ipython
• cython
• pandas
• pygp
• sphinx

If you already have Python and pip installed, probably pip will take care of installing all the dependencies. If you don’t know how to install these libraries, perhaps the easiest way is to download the Entougth Python Distribution.

Installing PANAMA and LIMMI

There are two options:

1. Running pip install panama (easiest)
2. Download panama and pygp, extract them, and then run

sudo python setup.py install

in the “pygp” directory first, and then in the “panama” directory.

Data

This is the simulated data we used in the paper: simulated.zip

Thanks to Leonid Kruglyak, Erin Smith and Rachel Brem we can also provide the yeast dataset we used for most of our experiments: yeast_data.zip