A platform to visualize and analyze genome contact maps
Project description
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
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 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
Usage
gcMapExplorer [Command]
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for gcMapExplorer-1.0.7-cp36-cp36m-macosx_10_11_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8b1e7d343e835a9a84a171e201c0cf84a8687bc87f44ff3caca18375929f0e94 |
|
MD5 | ebbdfa34b9243ee6e58eaf2e3d5de41c |
|
BLAKE2b-256 | 450dde25eced630e8abb26dc88a940888dc8d17b9bfa55932aaea7778c70f581 |
Hashes for gcMapExplorer-1.0.7-cp35-cp35m-macosx_10_11_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c5d3d4e57ad798bbb6bbce4966e10b36a75462daf23cdbcb3b74c2aaeb4aa36e |
|
MD5 | 8b2a6a0f841432059e0c9aeb4b6f9c94 |
|
BLAKE2b-256 | b106f647233fdb58c0c7684854fc57593077e3db7eb7fb2bfa43f001d2a2e27b |
Hashes for gcMapExplorer-1.0.7-cp34-cp34m-macosx_10_11_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 84efb7e7d63c3053c9f09340973c06770a825330d867d4fbd27deb4573553c38 |
|
MD5 | ce9ef4b6572341e33c1c2e76ead84f88 |
|
BLAKE2b-256 | 35c675c7f7dcbf71858a4b7e242f8bbe348c235a89ea6d4051608c06b692f823 |