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 file format conversions
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
h5Converter: Interface to convert bigWig/wig/bed file to h5 file
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 : 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
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
To Launch Browser
Run gcMapExplorer browser command.
To Launch Normalizer
Run gcMapExplorer normalizer command.
To Launch Importer
Run gcMapExplorer importer command.
To get help for a command
Run gcMapExplorer <sub-commands> -h command. For examples:
gcMapExplorer normKR -h
gcMapExplorer coo2cmap -h
Project details
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