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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

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.

  • 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

Usage

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

  • 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

Project details


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