This is a python package to call collective chromatin interactions in one state and dynamics across multiple states from Hi-C data.
Call single state hichub:
python3 hichub_single_state.py
Options:
-h, --help show this help message and exit
-p <file>, --path=<file>
Input/output path
-n <file>, --name=<file>
Hic file name
-r <int>, --resolution=<int>
Resolution for the output hic file.
Call multiple states hichub:
python3 multiple.py
Options:
-h, --help show this help message and exit
-p <file>, --path=<file>
Input/output path
-n <file>, --names=<file>
HiC file names separated by comma
-N <file>, --norm=<file>
HiC matrix normalization (NONE/KR)
-c <int>, --nclusters=<int>
Number of clusters
-r <int>, --resolution=<int>
Resolution fof hic matrix