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 - It can be used to perform analysis by any mathematical operations through programming.

For more details, visit: gcMapExplorer Homepage

For Discussion and Questions, visit this forum

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 - 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.
• Command to convert juicebox/juicer hic format to gcmap.
• 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. 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:

Graphical User Interface Applications

Command	Function
browser	Interactive Browser for genomic contact maps
cmapImporter	Interface to import contact maps and datasets
cmapNormalizer	Interface to normalize contact maps
h5Converter	Interface to convert bigWig/wig/bed file to h5 file

Commands to import Hi-C data

Command	Function
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
hic2gcmap	Import hic to gcmap

Commands to convert bigWig/wig/bed to h5

Command	Function
bigwig2h5	Convert a bigWig file to HDF5 format h5 file
wig2h5	Convert a wig file to HDF5 format h5 file
bed2h5	Convert a bed file to HDF5 format h5 file
encode2h5	Download and convert ENCODE datasets to HDF5 format h5 files

Commands to normalize Hi-C map

Command	Function
normKR	Normalization using Knight-Ruiz matrix balancing
normVC	Normalization using Vanilla-Coverage method
normIC	Normalization using Iterative Correction
normMCFS	Scale maps using Median/Mean Contact Frequency

Commands for Analysis

Command	Function
corrBWcmaps	Calculate correlation between contact maps

Configuration utility

Command	Function
config	To print configuration file and clean scratch directory

Command help

Run gcMapExplorer <sub-commands> -h command.

For example:

• gcMapExplorer normKR -h
• gcMapExplorer coo2cmap -h