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Table 1 A comparison of HiC Analysis software algorithms and features

From: HiFive: a tool suite for easy and efficient HiC and 5C data analysis

Method Normalization algorithm Can account for distance Fend-level resolution Parallelizable
HiFive Matrix balancing X X X
  Binning X X X
  Probability X X X
HiCPipe Binning   X X
HiCNorm Poisson regression    
HiCLib Matrix balancing   X  
HiTCa Poisson regression    
  Matrix balancing   X  
HOMER Read coverage X   X
Hi-Corrector Matrix balancing   X X
  1. aThis method is an R-based implementation of HiCLib’s and HiCNorm’s normalization approaches