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Set of programs to process, analyze and visualize Hi-C data

Project description

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Set of programs to process, analyze and visualize Hi-C data

Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing,
analysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and
visualization of chromosome conformation data. HiCExplorer facilitates the creation of contact matrices, correction
of contacts, TAD detection, A/B compartments, merging, reordering or chromosomes, conversion from different formats including
`cooler <>`_ and detection of long-range contacts. Moreover, it allows the visualization of
multiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general
any type of genomic scores), long range contacts and the visualization of viewpoints.


Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke.
**"High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications**, Volume 9, Article number: 189 (2018), doi:

Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning.
**"Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization", Nucleic Acids Research**, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi:

.. image:: ./docs/images/hicex2.png


HiCExplorer is available as a **command line suite of tools** on this very GitHub repository and also on other platforms (detailed in *Installation* below).

A **Galaxy HiCExplorer version** is directly available to users at Training material is available at the `Galaxy Training Network <>`_,
while a Galaxy Tour is available `here <>`_ for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the `Docker Galaxy HiCExplorer GitHub repository <>`_. Finally, this Galaxy version is available on the `Galaxy Tool Shed <>`_ and on the corresponding `GitHub repository <>`_.


With version 2.0, HiCExplorer is available for Python 2 and Python 3 and can be installed via:

- Pip, Anaconda and GitHub for command line usage.
- Toolshed and Docker image for its integration on Galaxy servers.

There are many easy ways to install HiCExplorer. Details can be found
`here <>`_.

Command line version

Install with conda

The easiest way to install HiCExplorer is using `BioConda <>`_

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

Install with pip

$ pip install HiCExplorer

Install by cloning this repository

You can install any one of the HiCExplorer branches on command line
(linux/mac) by cloning this git repository :


$ git clone
$ cd HiCExplorer
$ python install

If you don't have root permission, you can set a specific folder using the ``--prefix`` option


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

Galaxy version

Install with Docker

Installation instructions as a Docker image can be followed at

Install with Tool Shed

Galaxy HiCExplorer is part of the `Galaxy Tool Shed <>`_ and can be installed from there to any Galaxy server following `this link <>`_.

Please visit our complete documentation `Here <>`_. This documentation is also available directly within `Galaxy <>`_.

Project details

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Files for HiCExplorer, version
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Filename, size HiCExplorer- (197.3 kB) File type Wheel Python version py2 Upload date Hashes View
Filename, size HiCExplorer- (199.5 kB) File type Wheel Python version py3 Upload date Hashes View

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