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

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  • 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)
    • 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.

  • Interface and commands to convert bigWig/wig/bed file to genomic track dataset h5 file.

  • Interface and commands for contact map Normalizations.

  • Publication ready images at one click.


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).


Screen snapshot of Genome Contact Map browser

Genome Contact Map browser

Screen snapshot of Axis Properties interface in Browser

Axis Properties interface in Browser

Screen snapshot of Importer Interface

gcmap Importer Interface

Screen snapshot of genomic track dataset converter

genomic track dataset converter Interface

Screen snapshot of normalizer interface

Contact map normalization Interface