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        "author": "Rajendra Kumar",
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            "Environment :: Console",
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            "Intended Audience :: End Users/Desktop",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Natural Language :: English",
            "Operating System :: MacOS",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "\n.. _browser: http://gcmapexplorer.readthedocs.io/en/latest/mapBrowser.html\n.. _genome contact map: http://gcmapexplorer.readthedocs.io/en/latest/about_gcmap_file.html\n.. _genomic track datasets: http://gcmapexplorer.readthedocs.io/en/latest/about_h5_file.html\n.. _Normalization of contact maps: http://gcmapexplorer.readthedocs.io/en/latest/cmapNormalization.html\n.. _convert bigWig/wig/bed file to genomic track dataset h5 file: http://gcmapexplorer.readthedocs.io/en/latest/about_h5_file.html#convert-bigwig-wig-bed-to-genomic-track-h5-file\n\n.. image:: https://travis-ci.org/rjdkmr/gcMapExplorer.svg?branch=master\n    :target: https://travis-ci.org/rjdkmr/gcMapExplorer\n\n\nGenome Contact Map Explorer - gcMapExplorer\n===========================================\n\nIt is a platform to visualize and analyze the contact maps that are generated from Hi-C experiments. This package is developed by considering the huge size of contact maps at very fine resolution. It contains\n\n* Graphical user interface - Several windows like applications to perform tasks (See below tables).\n* Command Line Interface - Several commands to perform tasks (See below tables).\n* `Application Programming Interface <http://gcmapexplorer.readthedocs.io/en/latest/apidoc/summary.html>`_\n  - It can be used to perform analysis by any mathematical operations through programming.\n\n\n**For more details, visit:** `gcMapExplorer Homepage <http://gcmapexplorer.readthedocs.io/>`_\n\n**For Discussion and Questions, visit** `this forum <https://groups.google.com/forum/#!forum/gcmapexplorer>`_\n\nFeatures\n--------\n\n* Support for **huge contact maps** - Use of Disk instead of RAM - Matrices/arrays are stored in Disks -\n  mathematical operations by directly reading/writing from/to Disks, **without loading them into RAM**\n* A browser_ with rich interfaces\n  for **Comparative** and **Interactive** visualization of **two dimensional contact maps** along\n  with **genomic datasets** such as produced by DNase-seq, ChIP-seq, RNA-seq etc.\n* Contact maps can be **zoomed in/out** from finest resolution to whole chromosome level.\n* Rich customizations of **color scale for contact maps** visualization\n* Rich customizations of **X- and Y- axis properties**.\n* **Save visualization states and view-points** for later browsing\n\n* `Normalization of contact maps`_ by\n    * **Iterative Correction** (IC)\n    * **Knight-Ruiz Matrix Balancing** (KR)\n    * **Vanilla-Coverage** (VC)\n    * **Distance-Frequency**\n\n* A **new file format** based on HDF5 for `genome contact map`_ and `genomic track datasets`_.\n    * **Portable**, **platform independent** and can be read through C/C++, JAVA, Python and R programming language.\n    * **Very fast to read** - fast browsing of contact maps and genomic datasets\n\n* Another file format for `chromosomal contact map <http://gcmapexplorer.readthedocs.io/en/latest/about_ccmap_file.html>`_\n  - much faster than above format to read/write but not compact. Suitable for performing calculations.\n* `A GUI interface and commands <http://gcmapexplorer.readthedocs.io/en/latest/about_gcmap_file.html#convert-hi-c-data-to-gcmap>`_\n  to convert Coordinate Sparse, Pair Coordinate Sparse, HOMER Interaction matrix, Bin-Contact formats into the new gcmap and ccmap formats.\n* Command `to convert juicebox/juicer hic format to gcmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/hic2gcmap.html>`_.\n* Interface and commands to `convert bigWig/wig/bed file to genomic track dataset h5 file`_.\n* Interface and commands for `Normalization of contact maps`_.\n* Publication ready images at one click.\n\n\nCitation\n--------\n\nRajendra Kumar, Haitham Sobhy, Per Stenberg and Ludvig Lizana.\n`Genome Contact Map Explorer - A platform for the comparison, interactive visualization and analysis of genome contact maps. <https://doi.org/10.1093/nar/gkx644>`_\n*Nucleic Acids Res.* (2017).\n\n\n\nInterfaces and Commands\n-----------------------\n\nUsage\n-----\n\nRun ``gcMapExplorer`` command on terminal to get list of all sub-commands.\n\n**Following sub-commands are available:**\n\n.. list-table:: Graphical User Interface Applications\n    :widths: 1, 4\n    :header-rows: 1\n    :name: gui-table\n\n    * - Command\n      - Function\n\n    * - browser_\n      - Interactive Browser for genomic contact maps\n\n    * - `cmapImporter <http://gcmapexplorer.readthedocs.io/en/latest/commands/cmapImporter.html>`_\n      - Interface to import contact maps and datasets\n\n    * - `cmapNormalizer <http://gcmapexplorer.readthedocs.io/en/latest/commands/cmapNormalizer.html>`_\n      - Interface to normalize contact maps\n\n    * - `h5Converter <http://gcmapexplorer.readthedocs.io/en/latest/commands/h5Converter.html>`_\n      - Interface to convert bigWig/wig/bed file to h5 file\n\n\n.. list-table::  Commands to import Hi-C data\n    :widths: 1, 4\n    :header-rows: 1\n    :name: import-hic-command-table\n\n    * - Command\n      - Function\n\n    * - `coo2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/coo2cmap.html>`_\n      - Import COO sparse matrix format to ccmap or gcmap\n\n    * - `pairCoo2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/pairCoo2cmap.html>`_\n      - Import map from files similar to paired COO format\n\n    * - `homer2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/homer2cmap.html>`_\n      - Import HOMER Hi-C interaction matrix to ccmap or gcmap\n\n    * - `bc2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/bc2cmap.html>`_\n      - Import Bin-Contact format files to ccmap or gcmap\n\n    * - `hic2gcmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/hic2gcmap.html>`_\n      - Import hic to gcmap\n\n\n.. list-table:: Commands to convert bigWig/wig/bed to h5\n    :widths: 1, 4\n    :header-rows: 1\n    :name: convert-to-h5-file-table\n\n    * - Command\n      - Function\n\n    * - `bigwig2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/bigWig2h5.html>`_\n      - Convert a bigWig file to HDF5 format h5 file\n\n    * - `wig2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/wig2h5.html>`_\n      - Convert a wig file to HDF5 format h5 file\n\n    * - `bed2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/bed2h5.html>`_\n      - Convert a bed file to HDF5 format h5 file\n\n    * - `encode2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/encode2h5.html>`_\n      - Download and convert ENCODE datasets to HDF5 format h5 files\n\n\n.. list-table:: Commands to normalize Hi-C map\n    :widths: 1, 4\n    :header-rows: 1\n    :name: normalize-maps-table\n\n    * - Command\n      - Function\n\n    * - `normKR <http://gcmapexplorer.readthedocs.io/en/latest/commands/normKR.html>`_\n      - Normalization using Knight-Ruiz matrix balancing\n\n    * - `normVC <http://gcmapexplorer.readthedocs.io/en/latest/commands/normVC.html>`_\n      - Normalization using Vanilla-Coverage method\n\n    * - `normIC <http://gcmapexplorer.readthedocs.io/en/latest/commands/normIC.html>`_\n      - Normalization using Iterative Correction\n\n    * - `normMCFS <http://gcmapexplorer.readthedocs.io/en/latest/commands/normMCFS.html>`_\n      - Scale maps using Median/Mean Contact Frequency\n\n\n.. list-table:: Commands for Analysis\n    :widths: 1, 4\n    :header-rows: 1\n\n    * - Command\n      - Function\n\n    * - corrBWcmaps\n      - Calculate correlation between contact maps\n\n\n.. list-table:: Configuration utility\n    :widths: 1, 4\n    :header-rows: 1\n\n    * - Command\n      - Function\n\n\n    * - `config <http://gcmapexplorer.readthedocs.io/en/latest/commands/config.html>`_\n      - To print configuration file and clean scratch directory\n\n\nCommand help\n------------\nRun ``gcMapExplorer <sub-commands> -h`` command.\n\nFor example:\n    * ``gcMapExplorer normKR -h``\n    * ``gcMapExplorer coo2cmap -h``\n\n\n",
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