How to use gcMapExplorer?¶

Several interfaces are available as following.

Graphical User Interface Applications - 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. Tutorial files with Jupyter-Notebooks can be downloaded from here.

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
hic2gcmap	Import hic to 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

Run gcMapExplorer <sub-commands> -h command.

For example: