Metadata-Version: 1.1
Name: HiCExplorer
Version: 2.2.1
Summary: Set of programs to process, analyze and visualize Hi-C data
Home-page: http://hicexplorer.readthedocs.io
Author: Fidel Ramirez, Vivek Bhardwaj, Björn Grüning, Joachim Wolff
Author-email: deeptools@googlegroups.com
License: LICENSE.txt
Description: .. image:: https://travis-ci.org/deeptools/HiCExplorer.svg?branch=master
           :target: https://travis-ci.org/deeptools/HiCExplorer
        .. image:: https://readthedocs.org/projects/hicexplorer/badge/?version=latest
           :target: http://hicexplorer.readthedocs.io/?badge=latest
        .. image:: https://anaconda.org/bioconda/hicexplorer/badges/installer/conda.svg
           :target: https://anaconda.org/bioconda/hicexplorer
        .. image:: https://quay.io/repository/biocontainers/hicexplorer/status
           :target: https://quay.io/repository/biocontainers/hicexplorer
        .. image:: https://badge.fury.io/py/HiCExplorer.svg
               :target: https://badge.fury.io/py/HiCExplorer
        
        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 <https://github.com/mirnylab/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
        
        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
        
        .. image:: ./docs/images/hicex2.png
        
        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 <http://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html>`_,
        while a Galaxy Tour is available `here <https://hicexplorer.usegalaxy.eu/tours/hixexplorer>`_ for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the `Docker Galaxy HiCExplorer GitHub repository <https://github.com/deeptools/docker-galaxy-hicexplorer>`_. Finally, this Galaxy version is available on the `Galaxy Tool Shed <https://toolshed.g2.bx.psu.edu/>`_ and on the corresponding `GitHub repository <https://github.com/galaxyproject/tools-iuc>`_.
        
        
        Installation
        ^^^^^^^^^^^^
        
        With version 2.0, HiCExplorer is available for Python 2 and Python 3 and can be installed via:
        
        -  Pip, 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 <https://hicexplorer.readthedocs.io/en/latest/content/installation.html>`_.
        
        Command line version
        ++++++++++++++++++++
        
        Install with conda
        __________________
        
        The easiest way to install HiCExplorer is using `BioConda <http://bioconda.github.io/>`_
        ::
        
           $ 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
        
        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 <https://toolshed.g2.bx.psu.edu/>`_ and can be installed from there to any Galaxy server following `this link <https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=f1554978eeb3da8b>`_.
        
        
        Documentation:
        ^^^^^^^^^^^^^^
        Please visit our complete documentation `Here <http://hicexplorer.readthedocs.org/>`_. This documentation is also available directly within `Galaxy <http://hicexplorer.usegalaxy.eu/>`_.
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
