From: Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Method name | Type | Base model | Specific features | Reference |
---|---|---|---|---|
Duan et al. 2010 | Global background | Binomial | Specifically designed for yeast genome | [121] |
Fit-Hi-C/FitHiC2 | Global background | Binomial | Spline fitting procedure, compatible with different formats | |
HOMER | Global background | Binomial | Highly compatible with the HOMER Hi-C analysis pipeline | [124] |
GOTHiC | Global background | Binomial | Use relative coverage to estimate biases | [125] |
FitHiChIP | Global background | Binomial | Specifically designed for HiChIP data | [126] |
HIPPIE | Global background | Negative binomial | Account for fragment length and distance biases | |
HiC-DC | Global background | Negative binomial | Use zero-inflated model | [128] |
HMRFBayesHiC | Global background | Negative binomial | Use hidden Markov random field model | [129] |
FastHiC | Global background | Negative binomial | An updated version of HMRFBayesHi, with improved computing speed | [130] |
MaxHiC | Global background | Negative binomial | Use ADAM algorithm, identify interactions with enrichment for regulatory elements | [131] |
CHiCAGO | Global background | Negative binomial | Specifically designed for CHi-C data | [132] |
ChiCMaxima | Global background | Local maxima | Specifically designed for CHi-C data, more stringent and robust when comparing biological replicates | [133] |
HICCUP | Local background | Local enrichment | Robust for finding chromatin loops | [3] |
cLoops | Local background | DBSCAN | Loop detection with less computational resource | [134] |
Automated identification of stripes | Local background | Local enrichment | Specifically designed to identify architectural stripes | [135] |