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, merging, reordering or chromosomes, conversion from different formats 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) and long range contacts.

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". bioRxiv 115063; doi: https://doi.org/10.1101/115063

HiCExplorer is available for:

• Command line usage (via pip/anaconda/github)
• Integration into Galaxy servers (via toolshed/API/web-browser)

There are many easy ways to install HiCExplorer. Details can be found here

The easiest way to install HiCExplorer is using BioConda

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

$ pip install HiCExplorer

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

$ git clone https://github.com/maxplanck-ie/HiCExplorer.git
$ cd HiCExplorer
$ python setup.py install

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

$ python setup.py install --prefix /User/Tools/hicexplorer

Please visit our complete documentation Here