Man pages for qunhualilab/hicrep
Measuring the reproducibility of Hi-C data
| bed2mat | converting 3-column contact matrix to squared HiC matrix |
| cool2matrix | converting cooler format to Hi-C matrices |
| depth.adj | Sequencing depth adjustment |
| fast.mean.filter | A fast mean filter algorithm to smooth a matrix |
| get.scc | calculate the stratum-adjusted correlation coefficient |
| hic2mat | extract HiC data from .hic file and convert it to squared HiC... |
| HiCR1 | HiCR1 |
| HiCR2 | HiCR2 |
| hicrep-package | HiCRep pipeline calculates reproducibility of Hi-C... |
| 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 |
