Skip to main content

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)

    • Vanilla-Coverage (VC)

    • 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 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.

  • 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.

Citation

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

Usage

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

Following sub-commands are available:

Graphical User Interface Applications

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

Commands to import Hi-C data

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

Commands to convert bigWig/wig/bed to h5

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

Commands to normalize Hi-C map

Command

Function

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

Commands for Analysis

Command

Function

corrBWcmaps

Calculate correlation between contact maps

Configuration utility

Command

Function

config

To print configuration file and clean scratch directory

Command help

Run gcMapExplorer <sub-commands> -h command.

For example:
  • gcMapExplorer normKR -h

  • gcMapExplorer coo2cmap -h

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

gcMapExplorer-1.0.24.tar.gz (629.5 kB view hashes)

Uploaded Source

Built Distributions

gcMapExplorer-1.0.24-cp36-cp36m-win_amd64.whl (997.0 kB view hashes)

Uploaded CPython 3.6m Windows x86-64

gcMapExplorer-1.0.24-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB view hashes)

Uploaded CPython 3.6m

gcMapExplorer-1.0.24-cp36-cp36m-macosx_10_12_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.6m macOS 10.12+ x86-64

gcMapExplorer-1.0.24-cp35-cp35m-win_amd64.whl (990.0 kB view hashes)

Uploaded CPython 3.5m Windows x86-64

gcMapExplorer-1.0.24-cp35-cp35m-manylinux1_x86_64.whl (1.9 MB view hashes)

Uploaded CPython 3.5m

gcMapExplorer-1.0.24-cp35-cp35m-macosx_10_12_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.5m macOS 10.12+ x86-64

gcMapExplorer-1.0.24-cp34-cp34m-win_amd64.whl (1.1 MB view hashes)

Uploaded CPython 3.4m Windows x86-64

gcMapExplorer-1.0.24-cp34-cp34m-manylinux1_x86_64.whl (1.9 MB view hashes)

Uploaded CPython 3.4m

gcMapExplorer-1.0.24-cp34-cp34m-macosx_10_12_x86_64.whl (1.0 MB view hashes)

Uploaded CPython 3.4m macOS 10.12+ x86-64

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page