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https://github.com/rjdkmr/gcMapExplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:
https://github.com/rjdkmr/gcMapExplorer

bioinformatics genomic-data-analysis hi-c

Last synced: 4 months ago
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Genome Contact Map Explorer - gcMapExplorer. Visit:

Lists

README 

        

.. _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 `_

  - It can be used to perform analysis by any mathematical operations through programming.



**For more details, visit:** `gcMapExplorer Homepage `_



**For Discussion and Questions, visit** `this forum `_



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**.

* **Save visualization states and view-points** for later browsing



* `Normalization of contact maps`_ by

    * **Iterative Correction** (IC)

    * **Knight-Ruiz Matrix Balancing** (KR)

    * **Vanilla-Coverage** (VC)

    * **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 `chromosomal contact map `_

  - much faster than above format to read/write but not compact. Suitable for performing calculations.

* `A GUI interface and commands `_

  to convert Coordinate Sparse, Pair Coordinate Sparse, HOMER Interaction matrix, Bin-Contact formats into the new gcmap and ccmap formats.

* Command `to convert juicebox/juicer hic format to gcmap `_.

* 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.



Citation

--------



Rajendra Kumar, Haitham Sobhy, Per Stenberg and Ludvig Lizana.

`Genome Contact Map Explorer - A platform for the comparison, interactive visualization and analysis of genome contact maps. `_

*Nucleic Acids Res.* (2017).



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 `_

      - Interface to import contact maps and datasets



    * - `cmapNormalizer `_

      - Interface to normalize contact maps



    * - `h5Converter `_

      - 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 `_

      - Import COO sparse matrix format to ccmap or gcmap



    * - `pairCoo2cmap `_

      - Import map from files similar to paired COO format



    * - `homer2cmap `_

      - Import HOMER Hi-C interaction matrix to ccmap or gcmap



    * - `bc2cmap `_

      - Import Bin-Contact format files to ccmap or gcmap



    * - `hic2gcmap `_

      - Import hic to 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 `_

      - Convert a bigWig file to HDF5 format h5 file



    * - `wig2h5 `_

      - Convert a wig file to HDF5 format h5 file



    * - `bed2h5 `_

      - Convert a bed file to HDF5 format h5 file



    * - `encode2h5 `_

      - 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 `_

      - Normalization using Knight-Ruiz matrix balancing



    * - `normVC `_

      - Normalization using Vanilla-Coverage method



    * - `normIC `_

      - Normalization using Iterative Correction



    * - `normMCFS `_

      - 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



.. list-table:: Configuration utility

    :widths: 1, 4

    :header-rows: 1



    * - Command

      - Function



    * - `config `_

      - To print configuration file and clean scratch directory



Command help

------------

Run ``gcMapExplorer  -h`` command.



For example:

    * ``gcMapExplorer normKR -h``

    * ``gcMapExplorer coo2cmap -h``