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
- :ref:`gui-table` - Several windows like applications to perform tasks.
- Application Programming Interface - It can be used to perform analysis by any mathematical operations through programming.
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.
- Normalization of contact maps by
- Iterative Correction (IC)
- Knight-Ruiz Matrix Balancing (KR)
- Vanilla-Coverage (VC)
- 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.
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).
.. py:module:: gcMapExplorer
.. toctree:: :maxdepth: 2 Requirements and Installation <install> How to use gcMapExplorer? <usage.rst> Genome Contact Map Browser <mapBrowser.rst> About file formats <file_formats> Normalization of Hi-C maps <cmapNormalization> Frequently asked questions <faq.rst> Download example datasets <dLcmaps> Summary of Python Modules <apidoc/summary> Examples using Python Modules <modules_examples/index> Python Modules documentation <apidoc/index>