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

With version 2.0 HiCExplorer is available for Python 2 and Python 3:

• 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/deeptools/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