Man pages for dozmorovlab/HiCdiff
HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets
| cooler | Hi-C data in the cooler format |
| cooler2sparse | Transform a .cool file to a sparse upper triangular matrix... |
| create.hic.table | Create hic.table object from a sparse upper triangular Hi-C... |
| full2sparse | Transfrom a full Hi-C contact matrix to a sparse upper... |
| hic_diff | Detect differences between two jointly normalized Hi-C... |
| HiCdiff-package | HiCdiff |
| hic_loess | Perform joint loess normalization on two Hi-C datasets |
| hic_simulate | Simulate a Hi-C matrix and perform hic_diff analysis on it |
| HMEC.chr10 | Hi-C data from HMEC cell line - chromosome 10 at 500kb... |
| HMEC.chr22 | Hi-C data from HMEC cell line - chromosome 22 at 500kb... |
| hmec.IS | Hi-C data from HMEC cell line - chromosome 22 at 500kb... |
| KRnorm | Performs KR (Knight-Ruiz) normalization on a Hi-C matrix |
| make_InteractionSet | Convert HiCdiff results to InteractionSet object |
| MA_norm | Perform MA normalization on a hic.table object |
| MD.plot1 | Visualize the MD plot before and after loess normalization |
| MD.plot2 | Visualize the MD plot. |
| NHEK.chr10 | Hi-C data from NHEK cell line - chromosome 10 at 500kb... |
| NHEK.chr22 | Hi-C data from NHEK cell line - chromosome 22 at 500kb... |
| nhek.IS | Hi-C data from NHEK cell line - chromosome 22 at 500kb... |
| remove_centromere | Function to remove centromere columns and rows from a full... |
| SCN | SCN normalization from Cournac 2012 |
| sim.other.methods | Compare other normalization methods on simulated data |
| sparse2full | Transform a sparse upper triangular matrix to a full Hi-C... |
