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A platform to visualize and analyze genome contact maps

Project description

https://travis-ci.org/rjdkmr/gcMapExplorer.svg?branch=master

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.
  • Normalization of contact maps by
    • Iterative Correction (IC)
    • Knight-Ruiz Matrix Balancing (KR)
    • 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 chormosomal 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.
  • 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.

Interfaces and Commands

Usage

Run gcMapExplorer command on terminal to get list of all sub-commands.

Following sub-commands are available:

<caption>Graphical User Interface Applications</caption>
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
<caption>Commands to import Hi-C data</caption>
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
<caption>Commands to convert bigWig/wig/bed to h5</caption>
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
<caption>Commands to normalize Hi-C map</caption>
Command Function
normKR Normalization using Knight-Ruiz matrix balancing
normIC Normalization using Iterative Correction
normMCFS Scale maps using Median/Mean Contact Frequency
<caption>Commands for Analysis</caption>
Command Function
corrBWcmaps Calculate correlation between contact maps

Command help

Run gcMapExplorer <sub-commands> -h command.

For example:
  • gcMapExplorer normKR -h
  • gcMapExplorer coo2cmap -h

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
gcMapExplorer-1.0.11-cp34-cp34m-macosx_10_11_x86_64.whl (794.0 kB) Copy SHA256 hash SHA256 Wheel cp34 Apr 21, 2017
gcMapExplorer-1.0.11-cp34-cp34m-win_amd64.whl (1.1 MB) Copy SHA256 hash SHA256 Wheel cp34 Apr 22, 2017
gcMapExplorer-1.0.11-cp35-cp35m-macosx_10_11_x86_64.whl (792.0 kB) Copy SHA256 hash SHA256 Wheel cp35 Apr 21, 2017
gcMapExplorer-1.0.11-cp35-cp35m-win_amd64.whl (997.0 kB) Copy SHA256 hash SHA256 Wheel cp35 Apr 22, 2017
gcMapExplorer-1.0.11-cp36-cp36m-macosx_10_11_x86_64.whl (800.4 kB) Copy SHA256 hash SHA256 Wheel cp36 Apr 21, 2017
gcMapExplorer-1.0.11-cp36-cp36m-win_amd64.whl (1.0 MB) Copy SHA256 hash SHA256 Wheel cp36 Apr 22, 2017
gcMapExplorer-1.0.11.tar.gz (352.8 kB) Copy SHA256 hash SHA256 Source None Apr 21, 2017

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