Table 1 Pipelines for single-cell chromatin structure sequencing data

NucProcess

Pipeline for scHi-C analysis

scHi-C

[31]

Python

https://github.com/TheLaueLab/nuc_processing

combinatorialHiC

Pipeline for sciHi-C analysis

sciHi-C

[21]

Python

https://github.com/VRam142/combinatorialHiC

scHiC

Pipeline for scHi-C analysis

scHi-C

[16]

R and Perl

https://github.com/tanaylab/schic2

Dip-C

Pipeline for Dip-C analysis

Dip-C

[14]

Python

https://github.com/tanlongzhi/dip-c

Hickit

Pipeline for Dip-C analysis

Dip-C

[14]

C

https://github.com/lh3/hickit

scHiCTools

Computational toolbox for analyzing scHi-C data

scHi-C

[43]

Python

https://github.com/liu-bioinfo-lab/scHiCTools

SnapHiC

Pipeline for scHi-C analysis

scHi-C

[41]

Python

https://github.com/HuMingLab/SnapHiC

SnapHiC2

Pipeline for scHi-C analysis

scHi-C

[44]

Python

https://github.com/HuMingLab/SnapHiC/releases/tag/v0.2.2

scDEC-Hi-C

Comprehensive single-cell Hi-C data analysis

scHi-C

[45]

Python

https://github.com/kimmo1019/scDEC-Hi-C