Table 6 Tools categories by methodology

A

Clustering based

i. LOOPbit [23]

ii. LASCA [24]

iii. cLoops [25]

iv. cLoops2 [26]

v. HiCCUPS [48]

B

Probability-based

i. HiCExplorer [27]

ii. HiC-ACT [28]

iii. FitHiC [29]

iv. FitHiC2 [30]

v. FitHiChIP [31]

vi. GOTHiC [32]

vii. HiC-DC [33]

viii. ZipHiC [34]

ix. NeoLoopFinder [35]

x. HMRF Bayesian caller [36]

C

Classification based

i. FIREcaller [37]

ii. Peakachu [38]

D

Computer vision based

i. Mustache [40]

ii. Chromosight [42]

iii. SIP & SIPMeta [41]

iv. DeepLoop [49]

E

Pile-up procedure based

i. Coolpup.py [39]