Table 2 Computational tools developed for scHi-C analysis

MBO

Inference 3D structure of chromosomes from single-cell Hi-C

Manifold-based optimization (MBO)

scHi-C

[46]

MATLAB

https://folk.universitetetioslo.no/jonaspau/mbo/

NucDynamics

Inference 3D structure of chromosomes from single-cell Hi-C

Force field approach integrating molecular dynamics and optimization

scHi-C

[31]

Python and Cython

https://github.com/TheLaueLab/nuc_dynamics

Lavaburst

Contact cluster identification

Network modularity score

scHi-C

[20]

Python

https://github.com/nvictus/lavaburst

scHiCNorm

Normalization of scHi-C data

Poisson and negative binomial model

scHi-C

[40]

R and Perl

http://dna.cs.miami.edu/scHiCNorm/

HiCRep + MDS

Embedding scHi-C data into two dimensions

HiCRep and multidimensional scaling (MDS)

scHi-C

[40]

scHiCluster

Clustering cell type-specific chromosome structural patterns

Linear convolution and random walk

scHi-C

[47]

Python

https://github.com/zhoujt1994/scHiCluster

SCL

Inference 3D structure of chromosomes from single-cell Hi-C

Cubic lattice representation of a chromosome 3D structure and contact matrix imputation based on a 2D Gaussian function

scHi-C

[48]

C++ 

http://dna.cs.miami.edu/SCL/

SIMBA3D

Inference 3D structure of chromosomes from single-cell Hi-C

Bayesian approach with bulk Hi-C prior and multiscale optimization

scHi-C

[49]

Python

https://github.com/nerettilab/SIMBA3D

GiniQC

Quantifying unevenness in the distribution of interchromosomal reads in the scHi-C contact matrix

Gini coefficient from cumulative distribution of trans read pairs

scHi-C

[38]

Python

https://github.com/4dn-dcic/GiniQC

Inter-chromosomal-interactions

Analyzing interchromosomal interaction of single-cell Hi-C data

Significant interchromosomal interactions were derived with assumption where trans in single cell follows Bernoulli trial

scHiC

[50]

Python

https://github.com/bignetworks2019/Inter-chromosomal-interactions

schic-topic-model

Distinguishing cell type differences

Latent Dirichlet allocation (LDA)

scHi-C

[13]

Python and R

https://github.com/khj3017/schic-topic-model

deTOKI

TAD-like domain (TLD) detection in single cell

Nonnegative matrix factorization (NMF)

scHi-C

[51]

Python

https://github.com/lixiaoms/TOKI

Si–C

Inference 3D structure of chromosomes from single-cell Hi-C

Bayesian theory framework and polymer physics

scHi-C

[52]

C

https://github.com/TheMengLab/Si-C/tree/master

DPDchrom

Inference 3D structure of chromosomes from single-cell Hi-C

Dissipative particle dynamics (DPD)

scHi-C

[53]

Fortran and Python

https://github.com/polly-code/DPDchrom

Higashi

Multiscale and integrative scHi-C analysis

Transformation of scHi-C data into a hypergraph and hypergraph neural network

scHi-C

[54]

Python

https://github.com/ma-compbio/Higashi

Fast-Higashi

Ultrafast and interpretable scHi-C analysis

Tensor decomposition and partial random walk

scHi-C

[55]

Python

https://github.com/ma-compbio/Fast-Higashi

BandNorm

Normalization of scHi-C data

Baseline scaling-based normalization

scHi-C

[39]

R

https://github.com/keleslab/BandNorm

scVI-3D

Deep generative model for scHi-C data

Nonlinear latent factor model and hierarchical generative model

scHi-C

[39]

Python

https://github.com/keleslab/scVI-3D

HiCS

Association between regulatory factor binding and chromatin domain

Hierarchical chromatin domain structure identification

scHi-C

[56]

Python

https://github.com/YusenYe/HiCS

scHi-Csim

Simulation of scHi-C data

Interval sampling of raw scHi-C data

scHi-C

[57]

Python

https://github.com/zhanglabtools/scHi-CSim

ScHiCEDRN

Imputation of single-cell Hi-C

Generative adversarial network (GAN)

scHi-C

[58]

Python

https://github.com/BioinfoMachineLearning/ScHiCEDRN

DeDoc2

TAD-like domain (TLD) detection in single cell

Seeking minimal structural entropy

scHi-C

[59]

Java

https://github.com/zengguangjie/deDoc2

SnapHiC-D

Differential chromatin contact from scHi-C

Random walk with restart (RWR) and two-sided two-sample t-test with Benjamini–Hochberg procedure (FDR)

scHi-C

[42]

Python

https://github.com/HuMingLab/SnapHiC-D

HiC-SGL

Imputation of single-cell Hi-C

Subgraph extraction and graph representation learning

scHi-C

[60]

Python

https://github.com/zhengjh39/HiC-SGL