| Graphical User Interfaces (GUI) |
| browser |
To browse contact maps with genomic datasets |
| cmapImporter |
To import or convert data files compatible with gcMapExplorer |
| cmapNormalizer |
To normalize contact maps with various methods |
| h5Converter |
To convert bigwig/wig/bed file to browser compatible hdf5 format |
| Commands for normalization of Hi-C maps |
| normKR |
Knight-Ruiz matrix balancing |
| normIC |
Iterative-correction matrix balancing |
| normMCFS |
Median contact frequency scaling |
| Commands to import contact map files |
| coo2cmap |
COO sparse matrix format to ccmap or gcmap formats |
| homer2cmap |
HOMER Hi-C matrix format to ccmap or gcmap files |
| bc2cmap |
Bin-Contact files pair to ccmap or gcmap format |
| pairCoo2cmap |
Paired COO sparse matrix format to ccmap or gcmap formats |
| Commands to convert genomic track files |
| bigwig2h5 |
bigwig format to browser compatible hdf5 format |
| wig2h5 |
wig format to browser compatible hdf5 format |
| bed2h5 |
bed format to browser compatible hdf5 format |
| encode2h5 |
Download and convert files from ENCODE portal |
