.. _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