HiCR1                   HiCR1
HiCR2                   HiCR2
MatToVec                Convert the HiC matrix format to vector format
depth.adj               Sequencing depth adjustment
get.scc                 calculate the stratum-adjusted correlation
                        coefficient
hicrep-package          HiCRep pipeline calculates reproducibility of
                        Hi-C intrachromosome data
htrain                  Train the smoothing parameter (neighborhood
                        size).
prep                    Pre-processing the Hi-C matrices
smoothMat               smooth the Hi-C matrix with mean filter
vstran                  Variance stablization transformation
