Set of programs to process, analyze and visualize Hi-C data
Project description
HiCExplorer
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.
Citation:
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: https://doi.org/10.1038/s41467-017-02525-w
Installation
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
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 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
Documentation:
Please visit our complete documentation Here
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