Intervene requires the following Python modules and R packages:

Install BEDTools

Intervene is using pybedtools, which is Python wrapper for BEDTools. So, BEDTools should be installed before using Intervene It’s recomended to have a latest version, but if you have an older version already install, it should be fine. Please read the instructions at to install BEDTools, and make sure it is on your path and you are able to call bedtools from any directory.

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 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 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 requires Python modules individually, you can use the following commands, else you can install Intervene directly.

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 requires two R packages, UpSetR
and corrplot for visualization. To install these open R/RStudio and use the following command.
install.packages(c("UpSetR", "corrplot"))

Install Intervene

You can install a stable version of Intervene by using pip from PyPi or a development version by using git from GitHub.

Install using pip

You can install InterVene either from PyPi using pip or install it from the source. Please make sure you have already installed the above mentioned python libraries required to run InterVene.

Install from PyPi:

pip install intervene

Install development version from GitHub

If you have git installed, use this:

git clone
cd intervene
python install