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A platform to visualize and analyze genome contact maps

Project 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**.
* **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 <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.
* Command `to convert juicebox/juicer hic format to gcmap <<http://gcmapexplorer.readthedocs.io/en/latest/commands/hic2gcmap.html>`_.
* 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. <https://doi.org/10.1093/nar/gkx644>`_
*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 <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

* - `hic2gcmap <http://gcmapexplorer.readthedocs.io/en/latest/commands/hic2gcmap.html>`_
- 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 <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

* - `normVC <http://gcmapexplorer.readthedocs.io/en/latest/commands/normVC.html>`_
- Normalization using Vanilla-Coverage method

* - `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


.. list-table:: Configuration utility
:widths: 1, 4
:header-rows: 1

* - Command
- Function


* - `config <http://gcmapexplorer.readthedocs.io/en/latest/commands/config.html>`_
- To print configuration file and clean scratch directory


Command help
------------
Run ``gcMapExplorer <sub-commands> -h`` command.

For example:
* ``gcMapExplorer normKR -h``
* ``gcMapExplorer coo2cmap -h``


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