Measuring the reproducibility of Hi-C data


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Documentation for package ‘hicrep’ version 1.4.0

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