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Table 1 Comparison of HiC-bench with published Hi-C analysis or visualization tools

From: HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

Hi-C tasks

HiC-bench

HiFive

Hi-Cpipe

HiCNorm

hiclib

HiTC

HOMER

Hi-Corrector

HiC-Pro

TADbit

HiCUP

HiC-Box

HiCdat

HIPPIE

Sushi

HiCPlotter

Alignment

x

 

x

 

x

   

x

x

x

x

 

x

  

Filtering

x

x

x

 

x

   

x

x

x

x

 

x

  

Genome browser tracks

x

               

Quality assessment plots

x

x

x

  

x

  

x

 

x

 

x

x

  

Contact matrices

x

x

x

 

x

 

x

 

x

  

x

x

   

Matrix correction

x

x

 

x

x

x

x

x

x

x

 

x

x

   

Matrix comparison

x

           

x

   

Boundary scores

x

               

Domains

x

        

x

      

Boundary comparison

x

               

Specific interactions

x

 

x

 

x

 

x

 

x

 

x

x

x

x

  

Annotations

x

    

x

      

x

   

Allele-specific interactions

        

x

 

x

     

Visualization

x

x

x

  

x

x

     

x

 

x

x

Integration with ChIP-seq data

x

           

x

x

  

Parallelization

x

x

x

   

x

x

x

x

      

Integration of alternative tools

x

               

Parameter exploration

x

               

Reproducibility

x

x

              
  1. HiC-bench is a comprehensive and feature-rich Hi-C analysis pipeline that performs various Hi-C tasks by combining our newly-developed tools with existing tools
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