A platform to visualize and analyze genome contact maps
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)
- 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
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