{ "info": { "author": "Fidel Ramirez, Vivek Bhardwaj, Bj\u00f6rn Gr\u00fcning, Joachim Wolff", "author_email": "deeptools@googlegroups.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": ".. image:: https://travis-ci.org/deeptools/HiCExplorer.svg?branch=master\n :target: https://travis-ci.org/deeptools/HiCExplorer\n.. image:: https://readthedocs.org/projects/hicexplorer/badge/?version=latest\n :target: http://hicexplorer.readthedocs.io/?badge=latest\n.. image:: https://anaconda.org/bioconda/hicexplorer/badges/installer/conda.svg\n :target: https://anaconda.org/bioconda/hicexplorer\n.. image:: https://quay.io/repository/biocontainers/hicexplorer/status\n :target: https://quay.io/repository/biocontainers/hicexplorer\n.. image:: https://badge.fury.io/py/HiCExplorer.svg\n :target: https://badge.fury.io/py/HiCExplorer\n\nHiCExplorer\n===========\n\nSet of programs to process, analyze and visualize Hi-C data\n-----------------------------------------------------------\n\nSequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing,\nanalysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and\nvisualization of chromosome conformation data. HiCExplorer facilitates the creation of contact matrices, correction\nof contacts, TAD detection, A/B compartments, merging, reordering or chromosomes, conversion from different formats including\n`cooler `_ and detection of long-range contacts. Moreover, it allows the visualization of\nmultiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general\nany type of genomic scores), long range contacts and the visualization of viewpoints.\n\n\nCitation:\n^^^^^^^^^\n\n\nFidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke.\n**\"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\n\nJoachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ram\u00edrez, Bj\u00f6rn A Gr\u00fcning. \n**\"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\u2013W16, doi: https://doi.org/10.1093/nar/gky504\n\n.. image:: ./docs/images/hicex2.png\n\nAvailability\n^^^^^^^^^^^^\n\nHiCExplorer is available as a **command line suite of tools** on this very GitHub repository and also on other platforms (detailed in *Installation* below).\n\nA **Galaxy HiCExplorer version** is directly available to users at http://hicexplorer.usegalaxy.eu. Training material is available at the `Galaxy Training Network `_,\nwhile 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 `_.\n\n\nInstallation\n^^^^^^^^^^^^\n\nWith version 2.0, HiCExplorer is available for Python 2 and Python 3 and can be installed via:\n\n- Pip, Anaconda and GitHub for command line usage.\n- Toolshed and Docker image for its integration on Galaxy servers.\n\nThere are many easy ways to install HiCExplorer. Details can be found\n`here `_.\n\nCommand line version\n++++++++++++++++++++\n\nInstall with conda\n__________________\n\nThe easiest way to install HiCExplorer is using `BioConda `_\n::\n\n $ conda install hicexplorer -c bioconda -c conda-forge\n\nInstall with pip\n________________\n::\n\n $ pip install HiCExplorer\n\nInstall by cloning this repository\n__________________________________\n\nYou can install any one of the HiCExplorer branches on command line\n(linux/mac) by cloning this git repository :\n\n::\n\n $ git clone https://github.com/deeptools/HiCExplorer.git\n $ cd HiCExplorer\n $ python setup.py install\n\nIf you don't have root permission, you can set a specific folder using the ``--prefix`` option\n\n::\n\n\t$ python setup.py install --prefix /User/Tools/hicexplorer\n\nGalaxy version\n++++++++++++++\n\nInstall with Docker\n___________________\n\nInstallation instructions as a Docker image can be followed at https://github.com/deeptools/docker-galaxy-hicexplorer.\n\n\nInstall with Tool Shed\n______________________\n\nGalaxy HiCExplorer is part of the `Galaxy Tool Shed `_ and can be installed from there to any Galaxy server following `this link `_.\n\n\nDocumentation:\n^^^^^^^^^^^^^^\nPlease visit our complete documentation `Here `_. This documentation is also available directly within `Galaxy `_.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://hicexplorer.readthedocs.io", "keywords": "", "license": "LICENSE.txt", "maintainer": "", "maintainer_email": "", "name": "HiCExplorer", "package_url": "https://pypi.org/project/HiCExplorer/", "platform": "", "project_url": "https://pypi.org/project/HiCExplorer/", "project_urls": { "Homepage": "http://hicexplorer.readthedocs.io" }, "release_url": "https://pypi.org/project/HiCExplorer/2.2.1.1/", "requires_dist": [ "numpy (>=1.15.*)", "scipy (>=1.1.*)", "matplotlib (>2.2.*)", "pysam (>=0.14)", "intervaltree (==2.1.*)", "biopython (>=1.72)", "tables (>=3.4.*)", "pandas (>=0.23.*)", "pyBigWig (>=0.3.*)", "six (>=1.11.*)", "future (>=0.17.*)", "cooler (==0.8.2)", "jinja2 (>=2.10.*)", "unidecode (>=1.0.*)", "hicmatrix (>=7)", "pygenometracks (>=2.1)", "psutil (>=5.4.8)", "hic2cool (>=0.4)", "configparser (==3.5.*)" ], "requires_python": "", "summary": "Set of programs to process, analyze and visualize Hi-C data", "version": "2.2.1.1" }, "last_serial": 4819922, "releases": { "1.0": [ { "comment_text": "", "digests": { "md5": "8b7dca952f54b57b826cbcfe59e70be7", "sha256": "9e8f112de0d5efda8f9f795d80708658be1af33ca243b49883c2c507648d60a3" }, "downloads": -1, "filename": "HiCExplorer-1.0.tar.gz", "has_sig": false, "md5_digest": "8b7dca952f54b57b826cbcfe59e70be7", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 143051, "upload_time": "2017-11-24T13:17:26", "url": "https://files.pythonhosted.org/packages/13/3c/466b48c45c8eb3bcbef46e9efffe067b97cd00cbb177a046de0c7247011d/HiCExplorer-1.0.tar.gz" } ], "1.3": [ { "comment_text": "", "digests": { "md5": "bf1596ebcf6718fb160356afb8d29323", "sha256": "48badf9d623ce5c5b8394c01e33be7979f26975ecedad3a089e9322d8316f797" }, "downloads": -1, "filename": "HiCExplorer-1.3-py2.7.egg", "has_sig": false, "md5_digest": "bf1596ebcf6718fb160356afb8d29323", "packagetype": "bdist_egg", "python_version": "2.7", "requires_python": null, "size": 386387, "upload_time": "2017-11-24T13:17:28", "url": "https://files.pythonhosted.org/packages/26/93/b6bc55ccc310df3d7fd8f88ace772435b09e32ab149286075723976bbc1d/HiCExplorer-1.3-py2.7.egg" } ], "1.7": [ { "comment_text": "", "digests": { "md5": "1fc0e7899919a1177d34a288d54d6075", "sha256": "f21ac6600936c3135df7738fafd6219b44e6c0ec4c2f36aa630d04f07fb6ae64" }, "downloads": -1, "filename": "HiCExplorer-1.7.tar.gz", "has_sig": false, "md5_digest": "1fc0e7899919a1177d34a288d54d6075", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 114118, "upload_time": "2017-03-28T12:22:19", "url": "https://files.pythonhosted.org/packages/5f/d5/6ef7edb2f5285b32ae4939df1991d48dc79d04c3a57bf83f85542bd1f46f/HiCExplorer-1.7.tar.gz" } ], "1.7.1": [ { "comment_text": "", "digests": { "md5": "57617725cd581956c5e93344c7868a22", "sha256": "164e297abec240519f6dcd1d587a40b25df5569813a508160d5e246692ff5dcb" }, "downloads": -1, "filename": "HiCExplorer-1.7.1.tar.gz", "has_sig": false, "md5_digest": "57617725cd581956c5e93344c7868a22", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 118427, "upload_time": "2017-03-28T12:33:03", "url": "https://files.pythonhosted.org/packages/d0/f7/e8412cbf00ec1b8a58e33a97d002f312d9ed0e0c34af86254cb650e7bb5a/HiCExplorer-1.7.1.tar.gz" } ], "1.7.2": [ { "comment_text": "", "digests": { "md5": "d8d8c538f466a4bf898949aba8005be2", "sha256": "06d6750068dcbbf1f9a13343bfea78f9b1ff114444beef5c9774837380560ea4" }, "downloads": -1, "filename": "HiCExplorer-1.7.2.tar.gz", "has_sig": false, "md5_digest": "d8d8c538f466a4bf898949aba8005be2", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 122698, "upload_time": "2017-04-03T09:37:03", "url": "https://files.pythonhosted.org/packages/10/8e/60044ac31a7a776beed5f92f66eef91c2ad137b3282fb0547c18cccfa72d/HiCExplorer-1.7.2.tar.gz" } ], "1.8": [ { "comment_text": "", "digests": { "md5": "c53409dd384dc4aa4de3bc128271f922", "sha256": "0f6482a3d796b989e1af7c31741253d90a8e31d2767ca6ea5ece79afe72e97aa" }, "downloads": -1, "filename": "HiCExplorer-1.8.tar.gz", "has_sig": false, "md5_digest": "c53409dd384dc4aa4de3bc128271f922", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 129642, "upload_time": "2017-11-06T15:04:06", "url": "https://files.pythonhosted.org/packages/ff/bf/f9f2508af18d30d48742c68967c8b08dff077bdb99d3fe1e9fe77914d4e6/HiCExplorer-1.8.tar.gz" } ], "1.8.1": [ { "comment_text": "", "digests": { "md5": "c9550af67a116338c214b1eff160cc6d", "sha256": "e919ae499ae96dd11a867cae07ae92a60d149412386919ad54e5cc583ad3d972" }, "downloads": -1, "filename": "HiCExplorer-1.8.1.tar.gz", "has_sig": false, "md5_digest": "c9550af67a116338c214b1eff160cc6d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 130571, "upload_time": "2017-11-24T13:18:15", "url": "https://files.pythonhosted.org/packages/01/4a/326fe4e96b618b240c640ccd4d4430cdd76b368ed299e7375de0e490c91a/HiCExplorer-1.8.1.tar.gz" } ], "2.1.1": [ { "comment_text": "", "digests": { "md5": "cba3866e2650d79d155e23ed8c9daa4c", "sha256": "56d0ecabe8a84b4c240d641899c0116f2007d902c2d30fce1e7210a272b13e2a" }, "downloads": -1, "filename": "HiCExplorer-2.1.1.tar.gz", "has_sig": false, "md5_digest": "cba3866e2650d79d155e23ed8c9daa4c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 154990, "upload_time": "2018-03-27T10:35:33", "url": "https://files.pythonhosted.org/packages/3d/37/6697377a651a01fec58b81b54f959a6f33132bc9874108bb8ff2fe13b22b/HiCExplorer-2.1.1.tar.gz" } ], "2.2.1": [ { "comment_text": "", "digests": { "md5": "e892c35894cdc2fc774828dec8227de9", "sha256": "6ddeb6f90529d51b7b805eade7de9e2ecf9fdf91f303784681d88bf553349512" }, "downloads": -1, "filename": "HiCExplorer-2.2.1-py2-none-any.whl", "has_sig": false, "md5_digest": "e892c35894cdc2fc774828dec8227de9", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 146014, "upload_time": "2019-02-13T11:19:15", "url": "https://files.pythonhosted.org/packages/28/60/411036abf4c300a01d2c40f26260e1725c7a35de38f2e7e3585df89b370d/HiCExplorer-2.2.1-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "ad307c1520c6f688d9c04288df50679a", "sha256": "6deb9bd187b0afebe0f23bde97dfa787772d6e3873d084b33a7269f1422be370" }, "downloads": -1, "filename": "HiCExplorer-2.2.1.tar.gz", "has_sig": false, "md5_digest": "ad307c1520c6f688d9c04288df50679a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 107971, "upload_time": "2019-02-13T11:19:17", "url": "https://files.pythonhosted.org/packages/9a/97/2e07f963e322416759cb3307f35e05737bb7a9b309c50082e4e934043ca7/HiCExplorer-2.2.1.tar.gz" } ], "2.2.1.1": [ { "comment_text": "", "digests": { "md5": "cc458d47f54cf618a774d8c3fb48e6cd", "sha256": "30ec9606f47c8e356be7c9d7a01691775367a5a063f4c6b43f84652ea37f694d" }, "downloads": -1, "filename": "HiCExplorer-2.2.1.1-py2-none-any.whl", "has_sig": false, "md5_digest": "cc458d47f54cf618a774d8c3fb48e6cd", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 197302, "upload_time": "2019-02-14T11:30:04", "url": "https://files.pythonhosted.org/packages/1f/3e/44e2fa472443d2e17e5939e4160948ce2b2fa7b2fd8d0ee69ce297f7cda9/HiCExplorer-2.2.1.1-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "0747df9da5e7dfbac8feae457a6e07af", "sha256": "128b64d6d1634e0826cb3dcfc662468d2a880ed2f24ccdda3bff7a6ed376b89c" }, "downloads": -1, "filename": "HiCExplorer-2.2.1.1-py3-none-any.whl", "has_sig": false, "md5_digest": "0747df9da5e7dfbac8feae457a6e07af", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 199473, "upload_time": "2019-02-14T11:30:06", "url": "https://files.pythonhosted.org/packages/28/0f/271eb6ec4faf5cf880dc0a947e02476c4d600646f9e14dfb7d9002fa8d0a/HiCExplorer-2.2.1.1-py3-none-any.whl" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "cc458d47f54cf618a774d8c3fb48e6cd", "sha256": "30ec9606f47c8e356be7c9d7a01691775367a5a063f4c6b43f84652ea37f694d" }, "downloads": -1, "filename": "HiCExplorer-2.2.1.1-py2-none-any.whl", "has_sig": false, "md5_digest": "cc458d47f54cf618a774d8c3fb48e6cd", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 197302, "upload_time": "2019-02-14T11:30:04", "url": "https://files.pythonhosted.org/packages/1f/3e/44e2fa472443d2e17e5939e4160948ce2b2fa7b2fd8d0ee69ce297f7cda9/HiCExplorer-2.2.1.1-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "0747df9da5e7dfbac8feae457a6e07af", "sha256": "128b64d6d1634e0826cb3dcfc662468d2a880ed2f24ccdda3bff7a6ed376b89c" }, "downloads": -1, "filename": "HiCExplorer-2.2.1.1-py3-none-any.whl", "has_sig": false, "md5_digest": "0747df9da5e7dfbac8feae457a6e07af", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 199473, "upload_time": "2019-02-14T11:30:06", "url": "https://files.pythonhosted.org/packages/28/0f/271eb6ec4faf5cf880dc0a947e02476c4d600646f9e14dfb7d9002fa8d0a/HiCExplorer-2.2.1.1-py3-none-any.whl" } ] }