How to use gcMapExplorer?

Several interfaces are available as following.


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