Metadata-Version: 1.1
Name: gcMapExplorer
Version: 1.0.11
Summary: A platform to visualize and analyze genome contact maps
Home-page: https://github.com/rjdkmr/gcMapExplorer
Author: Rajendra Kumar
Author-email: rjdkmr@gmail.com
License: GNU General Public License v3 (GPLv3)
Description: 
        .. _browser: http://gcmapexplorer.readthedocs.io/en/latest/mapBrowser.html
        .. _genome contact map: http://gcmapexplorer.readthedocs.io/en/latest/about_gcmap_file.html
        .. _genomic track datasets: http://gcmapexplorer.readthedocs.io/en/latest/about_h5_file.html
        .. _Normalization of contact maps: http://gcmapexplorer.readthedocs.io/en/latest/cmapNormalization.html
        .. _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
        
        .. image:: https://travis-ci.org/rjdkmr/gcMapExplorer.svg?branch=master
            :target: https://travis-ci.org/rjdkmr/gcMapExplorer
        
        
        Genome Contact Map Explorer - gcMapExplorer
        ===========================================
        
        It 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
        
        * Graphical user interface - Several windows like applications to perform tasks (See below tables).
        * Command Line Interface - Several commands to perform tasks (See below tables).
        * `Application Programming Interface <http://gcmapexplorer.readthedocs.io/en/latest/apidoc/summary.html>`_
          - It can be used to perform analysis by any mathematical operations through programming.
        
        
        **For more details, visit:** `gcMapExplorer Homepage <http://gcmapexplorer.readthedocs.io/>`_
        
        **For Discussion and Questions, visit** `this forum <https://groups.google.com/forum/#!forum/gcmapexplorer>`_
        
        Features
        --------
        
        * Support for **huge contact maps** - Use of Disk instead of RAM - Matrices/arrays are stored in Disks -
          mathematical operations by directly reading/writing from/to Disks, **without loading them into RAM**
        * A browser_ with rich interfaces
          for **Comparative** and **Interactive** visualization of **two dimensional contact maps** along
          with **genomic datasets** such as produced by DNase-seq, ChIP-seq, RNA-seq etc.
        * Contact maps can be **zoomed in/out** from finest resolution to whole chromosome level.
        * Rich customizations of **color scale for contact maps** visualization
        * Rich customizations of **X- and Y- axis properties**.
        
        * `Normalization of contact maps`_ by
            * **Iterative Correction** (IC)
            * **Knight-Ruiz Matrix Balancing** (KR)
            * **Distance-Frequency**
        
        * A **new file format** based on HDF5 for `genome contact map`_ and `genomic track datasets`_.
            * **Portable**, **platform independent** and can be read through C/C++, JAVA, Python and R programming language.
            * **Very fast to read** - fast browsing of contact maps and genomic datasets
        
        * Another file format for `chormosomal contact map <http://gcmapexplorer.readthedocs.io/en/latest/about_ccmap_file.html>`_
          - much faster than above format to read/write but not compact. Suitable for performing calculations.
        * `A GUI interface and commands <http://gcmapexplorer.readthedocs.io/en/latest/about_gcmap_file.html#convert-hi-c-data-to-gcmap>`_
          to convert Coordinate Sparse, Pair Coordinate Sparse, HOMER Interaction matrix, Bin-Contact formats into the new gcmap and ccmap formats.
        * Interface and commands to `convert bigWig/wig/bed file to genomic track dataset h5 file`_.
        * Interface and commands for `Normalization of contact maps`_.
        * Publication ready images at one click.
        
        
        ----
        
        
        Interfaces and Commands
        -----------------------
        
        Usage
        -----
        
        Run ``gcMapExplorer`` command on terminal to get list of all sub-commands.
        
        **Following sub-commands are available:**
        
        .. list-table:: Graphical User Interface Applications
            :widths: 1, 4
            :header-rows: 1
            :name: gui-table
        
            * - Command
              - Function
        
            * - browser_
              - Interactive Browser for genomic contact maps
        
            * - `cmapImporter <http://gcmapexplorer.readthedocs.io/en/latest/commands/cmapImporter.html>`_
              - Interface to import contact maps and datasets
        
            * - `cmapNormalizer <http://gcmapexplorer.readthedocs.io/en/latest/commands/cmapNormalizer.html>`_
              - Interface to normalize contact maps
        
            * - `h5Converter <http://gcmapexplorer.readthedocs.io/en/latest/commands/h5Converter.html>`_
              - Interface to convert bigWig/wig/bed file to h5 file
        
        
        .. list-table::  Commands to import Hi-C data
            :widths: 1, 4
            :header-rows: 1
            :name: import-hic-command-table
        
            * - Command
              - Function
        
            * - `coo2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/coo2cmap.html>`_
              - Import COO sparse matrix format to ccmap or gcmap
        
            * - `pairCoo2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/pairCoo2cmap.html>`_
              - Import map from files similar to paired COO format
        
            * - `homer2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/homer2cmap.html>`_
              - Import HOMER Hi-C interaction matrix to ccmap or gcmap
        
            * - `bc2cmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/bc2cmap.html>`_
              - Import Bin-Contact format files to ccmap or gcmap
        
        
        .. list-table:: Commands to convert bigWig/wig/bed to h5
            :widths: 1, 4
            :header-rows: 1
            :name: convert-to-h5-file-table
        
            * - Command
              - Function
        
            * - `bigwig2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/bigWig2h5.html>`_
              - Convert a bigWig file to HDF5 format h5 file
        
            * - `wig2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/wig2h5.html>`_
              - Convert a wig file to HDF5 format h5 file
        
            * - `bed2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/bed2h5.html>`_
              - Convert a bed file to HDF5 format h5 file
        
            * - `encode2h5 <http://gcmapexplorer.readthedocs.io/en/latest/commands/encode2h5.html>`_
              - Download and convert ENCODE datasets to HDF5 format h5 files
        
        
        .. list-table:: Commands to normalize Hi-C map
            :widths: 1, 4
            :header-rows: 1
            :name: normalize-maps-table
        
            * - Command
              - Function
        
            * - `normKR <http://gcmapexplorer.readthedocs.io/en/latest/commands/normKR.html>`_
              - Normalization using Knight-Ruiz matrix balancing
        
            * - `normIC <http://gcmapexplorer.readthedocs.io/en/latest/commands/normIC.html>`_
              - Normalization using Iterative Correction
        
            * - `normMCFS <http://gcmapexplorer.readthedocs.io/en/latest/commands/normMCFS.html>`_
              - Scale maps using Median/Mean Contact Frequency
        
        
        .. list-table:: Commands for Analysis
            :widths: 1, 4
            :header-rows: 1
        
            * - Command
              - Function
        
            * - corrBWcmaps
              - Calculate correlation between contact maps
        
        
        Command help
        ------------
        Run ``gcMapExplorer <sub-commands> -h`` command.
        
        For example:
        	* ``gcMapExplorer normKR -h``
        	* ``gcMapExplorer coo2cmap -h``
        
Keywords: Hi-C,Genome Contact Map Explorer,Contact Map Explorer,3D Genome Organization
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Environment :: X11 Applications :: Qt
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
