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A platform to visualize and analyze genome contact maps

Project Description

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


  • 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


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
  • 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
  • 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
Release History

Release History

This version
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