HiCExplorer 1.8.1

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, 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.

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

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

$ pip install HiCExplorer

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

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