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 Hi-C Explorer, a set of tools for the analysis and visualization of chromosome conformation data. Hi-C explorer 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
Installation
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
Install with conda
The easiest way to install HiCExplorer is using BioConda
$ conda install -c bioconda hicexplorer
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/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
Documentation:
Please visit our complete documentation Here
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