• python >= 3.6

  • numpy >= 1.19.*

  • scipy >= 1.5.*

  • matplotlib-base >= 3.1.*

  • ipykernel >= 5.3.0

  • pysam >= 0.16.*

  • intervaltree >= 3.1.*

  • biopython

  • pytables >= 3.6.*

  • pandas >= 1.1.*

  • pybigwig >= 0.3.*

  • jinja2 >= 2.11

  • unidecode >= 1.1.*

  • hicmatrix >= 15

  • hic2cool >= 0.8.3

  • psutil >= 5.7.*

  • pygenometracks >= 3.5

  • fit_nbinom >= 1.1

  • cooler >= 0.8.10

  • krbalancing >= 0.0.5 (Needs the library eigen; openmp is recommended for linux users. No openmp support on macOS.)

  • pybedtools >= 0.8.*

  • future >= 0.18

  • tqdm >= 4.50

  • hyperopt >= 0.2.4

  • python-graphviz >= 0.14

Warning: Python 2.7 support is discontinued. Moreover, the support for pip is discontinued too. Warning: We strongly recommend to use the conda package manager and will no longer give support on all issues raising with pip.

Command line installation using conda

The fastet way to obtain Python 3.6 or 3.7 together with numpy and scipy is via the Anaconda Scientific Python Distribution. Just download the version that’s suitable for your operating system and follow the directions for its installation. All of the requirements for HiCExplorer can be installed in Anaconda with:

$ conda install hicexplorer -c bioconda -c conda-forge

We strongly recommended to use conda to install HiCExplorer.

Command line installation using pip

The installation via pip is discontinued with version 3.0. The reason for this is that we want to provide a ‘one-click’ installation. However, with version 3.0 we added the C++ library eigen as dependency and pip does not support non-Python packages.

For older versions you can still use pip: Install HiCExplorer using the following command:

$ pip install hicexplorer

All python requirements should be automatically installed.

If you need to specify a specific path for the installation of the tools, make use of pip install’s numerous options:

$ pip install --install-option="--prefix=/MyPath/Tools/hicexplorer" git+

Warning: It can be that you have to install additional packages via your system package manager to successfully install HiCExplorer via pip. Warning: We strongly recommend to use the conda package manager and will no longer give support on all issues raising with pip.

Command line installation without pip

You are highly recommended to use pip rather than these more complicated steps.

  1. Install the requirements listed above in the “requirements” section. This is done automatically by pip.

2. Download source code

$ git clone

or if you want a particular release, choose one from

$ wget
$ tar -xzvf

3. To install the source code (if you don’t have root permission, you can set a specific folder using the --prefix option)

$ python install --prefix /User/Tools/hicexplorer

Galaxy installation

HiCExplorer can be easily integrated into a local Galaxy, the wrappers are provided at the Galaxy tool shed.

Installation with Docker

The HiCExplorer Galaxy instance is also available as a docker container, for those wishing to use the Galaxy framework but who also prefer a virtualized solution. This container is quite simple to install:

$ sudo docker pull

To start and otherwise modify this container, please see the instructions on the docker-galaxy-stable github repository. Note that you must use bgruening/galaxy-hicexplorer in place of bgruening/galaxy-stable in the examples, as the HiCExplorer Galaxy container is built on top of the galaxy-stable container.


For support, or feature requests contact: