Metadata-Version: 1.1
Name: gcMapExplorer
Version: 1.0.2
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: 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.
          * Command Line Interface - Several commands to perform tasks.
          * Application Programming Interface - It can be used to perform analysis by any mathematical operations through programming.
        
        
        **For more details, visit:** `gcMapExplorer Homepage <http://gcmapexplorer.readthedocs.io/>`_
        
        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** for contact map  and genomic 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 - much faster than above format to read/write but not compact
        * Easy import of Coordinate Sparse, HOMER Interaction matrix and Bin-Contact formats to the new formats.
        * Interface for data conversion
        * Interface for Normalization
        * Publication ready images at one click.
        
        
        ----
        
        
        Interfaces and Commands
        -----------------------
        
        Usage
        ~~~~~
        
        ``gcMapExplorer [Command]``
        
        Run ``gcMapExplorer`` command on terminal to get list of all sub-commands.
        
        Following sub-commands are available:
        
        Graphical User Interface
        ~~~~~~~~~~~~~~~~~~~~~~~~
        * **browser** : Interactive Browser for genomic contact maps
        * **importer** : Interface to import contact maps and datasets
        * **normalizer** : Interface to normalize contact maps
        
        Commands to convert or import data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        * **coo2cmap** : Import COO sparse matrix format to ccmap or gcmap
        * **homer2cmap** : Import HOMER Hi-C interaction matrix to ccmap or gcmap
        * **bc2cmap** : Import Bin-Contact format files to ccmap or gcmap
        * **bigwig2h5** : Import a bigWig file to HDF5 format h5 file
        
        Commands to normalize contact map
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        * **normKR** : Normalization using Knight-Ruiz matrix balancing
        * **normIC** : Normalization using Iterative Correction
        * **normMCFS** : Normalization by Median Contact Frequency Scaling
        
        Commands for Analysis
        ~~~~~~~~~~~~~~~~~~~~~
        * **corrBWcmaps** : Calculate correlation between contact maps
        
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
