HiCExplorer 2.1.1

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

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

$ pip install HiCExplorer

$ git clone https://github.com/deeptools/HiCExplorer.git
$ cd HiCExplorer
$ python setup.py install

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