========== DISCOVER

DISCOVER is a novel statistical method for analysing co-occurrence and mutual exclusivity in cancer genomics data. The details of this method are described in our paper A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence (Genome Biology 2016 17:261_).

.. _Genome Biology 2016 17:261: https://dx.doi.org/10.1186/s13059-016-1114-x

Installation

DISCOVER is available for both Python and R.

Python

The easiest way to install the DISCOVER Python package is by using Miniconda_ or Anaconda_. We provide precompiled DISCOVER packages for 64-bit Linux, Windows, and Mac OS X. The following steps assume that Miniconda or Anaconda has been installed.

.. _Miniconda: https://docs.conda.io/en/latest/miniconda.html .. _Anaconda: https://www.anaconda.com/products/individual

To create a new conda environment containing DISCOVER and its dependencies, execute the following command in a terminal (Linux/Mac OS X) or command prompt (Windows).

::

conda create -n discover -c https://ccb.nki.nl/software/discover/repos/conda discover

This environment can be activated using:

::

conda activate discover

Note that this environment contains the bare minimum to use DISCOVER. It does not, for example, include IPython. Trying to run IPython anyway might start a version installed in a different environment, and hence, importing DISCOVER will not succeed. Consult the conda documentation_ to find out how to install additional packages (such as IPython). Alternatively, DISCOVER can be installed in an existing environment as follows.

::

conda install -c https://ccb.nki.nl/software/discover/repos/conda discover

.. _conda documentation: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html

Check the documentation_ for instructions on how to use this package.

R

We provide precompiled R packages for Windows and Mac OS X, as well as a source package for installation on Linux. Installation on Linux requires gfortran version 5.1 or later. To install the DISCOVER package, execute the following in an R session.

::

options(repos=c(getOption("repos"), "https://ccb.nki.nl/software/discover/repos/r")) install.packages("discover")

Check the documentation_ for instructions on how to use this package.

Documentation

• Python_
• R_

.. _Python: https://ccb.nki.nl/software/discover/doc/python .. _R: https://ccb.nki.nl/software/discover/doc/r/discover-intro.html