HiCExplorer

Set of programs to process, analyze and visualize Hi-C, Micro-C and cHi-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. With version 3.7.6 we introduce the support for Micro-C data for the build of matrices.

Single-cell Hi-C data

We provide the scHiCExplorer to create, manipulate, analyse and visualize single-cell Hi-C data in its own software: The scHiCExplorer.

Citation:

Joachim Wolff, Rolf Backofen, Björn Grüning. Loop detection using Hi-C data with HiCExplorer, GigaScience, Volume 11, 2022, giac061, https://doi.org/10.1093/gigascience/giac061

Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization, Nucleic Acids Research, Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W177–W184, https://doi.org/10.1093/nar/gkaa220

Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning. "Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization", Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504

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

Availability

HiCExplorer is available as a command line suite of tools on this very GitHub repository and also on other platforms (detailed in Installation below).

A Galaxy HiCExplorer version is directly available to users at http://hicexplorer.usegalaxy.eu. Training material is available at the Galaxy Training Network, while a Galaxy Tour is available here for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the Docker Galaxy HiCExplorer GitHub repository. Finally, this Galaxy version is available on the Galaxy Tool Shed and on the corresponding GitHub repository.

Installation

With version 3.0, HiCExplorer is available for Python 3 only, the Python 2 support is discontinued. HiCExplorer can be installed with conda.

• Anaconda and GitHub for command line usage.
• Toolshed and Docker image for its integration on Galaxy servers.

There are many easy ways to install HiCExplorer. Details can be found here.

We strongly recommended to use conda to install HiCExplorer.

Command line version

Install with conda

The easiest way to install HiCExplorer is using BioConda

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

We highly recommend conda environments to separate software from each other. With it, different versions of dependencies do not interfere with each other.

$ conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge
$ conda activate hicexplorer

To deactivate the environment use:

$ conda deactivate

To learn more about conda and environments, please consider the following documentation.

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

If you don't use conda, please take care of all dependencies on your own.

Galaxy version

Install with Docker

Installation instructions as a Docker image can be followed at https://github.com/deeptools/docker-galaxy-hicexplorer.

Install with Tool Shed

Galaxy HiCExplorer is part of the Galaxy Tool Shed and can be installed from there to any Galaxy server following this link.

Documentation:

Please visit our complete documentation Here. This documentation is also available directly within Galaxy.