Tools for Hi-C Anaylsis
| Program | Year | Pre-analysis | Interaction | TAD | 3D | Visual | Comments |
|---|---|---|---|---|---|---|---|
| Juicer | 2016 | map/flt/norm | Loop/HiCCUPS | Arrowhead | JuiceBox | Java/js/html5 | |
| hickit | map/flt | Loop | Yes | SC | 2D/3D | By me; C/js | |
| TADbit | 2017 | map/flt/norm | Yes | Yes | Python | ||
| HiCExplorer | map/flt/norm | Yes | 2D | Python | |||
| GITAR | 2018 | map/flt/norm | DI | 2D | Python | ||
| HiC-Bench | 2017 | map/flt/norm | Yes | C++ | |||
| dip-c | map/flt | SC | Python | ||||
| HIPPIE | 2015 | map/flt | Yes | ||||
| HiC-Pro | 2015 | map/flt/norm | |||||
| HiCapp | map/flt/norm | R | |||||
| HiCUP | Yes | ||||||
| HiFive | 2015 | Yes | Python | ||||
| HOMER | Yes | ||||||
| hiclib | Yes | Cython | |||||
| cLoops | Loop | Python | |||||
| CHiCAGO | 2016 | Yes | R | ||||
| GOTHiC | 2017 | Yes | R | ||||
| Fit-Hi-C | 2014 | Yes | Python | ||||
| TADtree | 2016 | Yes | Python | ||||
| HiCseg | 2014 | Yes | R | ||||
| Armatus | Yes | C++ | |||||
| GMAP | 2017 | Yes | R | ||||
| MOGEN | Yes | 3D | Java | ||||
| 3D-GNOME | 2016 | Yes | 3D | ||||
| nuc_dynamics | 2017 | SC | SC=single cell; Cython | ||||
| miniMDS | 2017 | Yes | |||||
| Chrom3D | 2017 | Yes | |||||
| Gen3D | 2015 | Yes | |||||
| HSA | 2016 | Yes | |||||
| ChromSDE | 2013 | Yes | |||||
| HiGlass | 2018 | 2D | js/html5 | ||||
| TADkit | Yes | js/html5 | |||||
| HiCPlotter | 2015 | 2D | Python | ||||
| GMOL | 2016 | 3D | Java |