A platform to visualize and analyze genome contact maps
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
- 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)
- 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.
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
Run gcMapExplorer command on terminal to get list of all sub-commands.
Following sub-commands are available:
|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|
|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|
|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|
|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|
|corrBWcmaps||Calculate correlation between contact maps|
|config||To print configuration file and clean scratch directory|
Run gcMapExplorer <sub-commands> -h command.
- For example:
- gcMapExplorer normKR -h
- gcMapExplorer coo2cmap -h
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