Intervene is available on PyPi, through Bioconda, and source code available on GitHub and Bitbucket. Intervene takes care of the installation of all the required Python modules. If you already have a working installation of Python, the easiest way to install the required Python modules is by installing Intervene using pip.

If you’re setting up Python for the first time, we recommend to install it using the Conda or Miniconda Python distribution. This comes with several helpful scientific and data processing libraries, and available for platforms including Windows, Mac OSX and Linux.

You can use one of the following ways to install Intervene.

Quick installation

Install uisng Conda

We highly recommend to install Intervene using Conda, this will take care of the dependencies. If you already have Conda or Miniconda installed, go ahead and use the below command.

conda install -c bioconda intervene


This will install all the dependencies and you are ready to use Intervene.

Install using pip

You can install Intervene from PyPi using pip.

pip install intervene


If you install using pip, make sure to install BEDTools and R packages listed below.


Intervene requires the following Python modules and R packages:

Install BEDTools

Intervene is using pybedtools, which is a Python wrapper for the BEDTools. BEDTools should be installed before using Intervene. It is recomended to have the latest version of the tool. Please read the installation instructions at to install BEDTools, and make sure it is accessible through your PATH variable.

Install required R packages

Intervene rquires three R packages, UpSetR , corrplot for visualization and Cairo to generate high-quality vector and bitmap figures. To install these, open R/RStudio and use the following command.

install.packages(c("UpSetR", "corrplot","Cairo"))

Install Intervene from source

You can install a development version by using git from our bitbucket repository at or Github.

Install development version from Bitbucket

If you have git installed, use this:

git clone
cd intervene
python sdist install

Install development version from GitHub

If you have git installed, use this:

git clone
cd intervene
python sdist install