Quick installation

Install uisng bioconda

conda install -c bioconda intervene

This will install all the dependencies and you are ready to use Intervene. Make sure you have R installed.

Install using pip

You can install Intervene from PyPi using pip.


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 Python modules

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 Anaconda Python distribution These come with several helpful scientific and data processing libraries. These are available for platforms including Windows, Mac OSX and Linux.

If you want to install the required Python modules manually, you can use the following commands.

Install pybedtools

Install it from PyPi

pip install pybedtools

or using conda

conda install -c bioconda pybedtools

Read more details about ''pybedtools'' installation:

Install Pandas

Install it from PyPi

pip install pandas

Or install with conda

conda install pandas

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