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| HiCcompare-package | HiCcompare |
| brain_table | Hi-C data from two regions of the brain at 100KB resolution |
| centromere_locations | Locations of the centromeres for hg19 |
| cooler | Hi-C data in the cooler format |
| cooler2bedpe | Read a .cool file into R and output the data in BEDPE format |
| cooler2sparse | Transform a .cool file to a sparse upper triangular matrix for input into hic_loess |
| create.hic.table | Create hic.table object from a sparse upper triangular Hi-C matrix |
| filter_params | Determine the A quantile cutoff to be used |
| full2sparse | Transfrom a full Hi-C contact matrix to a sparse upper triangular matrix |
| get_CNV | Function to get the locations of copy number variations |
| hg19_blacklist | BED file for hg19 blacklisted regions |
| hg38_blacklist | BED file for hg38 blacklisted regions |
| HiCcompare | HiCcompare |
| hicpro2bedpe | Convert HiC-Pro results to BEDPE format |
| hic_compare | Detect differences between two jointly normalized Hi-C datasets. |
| hic_diff | Detect differences between two jointly normalized Hi-C datasets. OLD METHOD; USE hic_compare() instead |
| hic_loess | Perform joint loess normalization on two Hi-C datasets |
| hic_simulate | Simulate a Hi-C matrix and perform HiCcompare analysis on it |
| HMEC.chr10 | Hi-C data from HMEC cell line - chromosome 10 at 500kb resolution |
| HMEC.chr22 | Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution |
| hmec.IS | Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution |
| KRnorm | Performs KR (Knight-Ruiz) normalization on a Hi-C matrix |
| make_InteractionSet | Convert HiCdiff results to InteractionSet object |
| manhattan_plot | Create a Manhattan plot for the results of HiCcompare |
| 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 resolution |
| NHEK.chr22 | Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution |
| nhek.IS | Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution |
| remove_centromere | Function to remove centromere columns and rows from a full Hi-C contact matrix |
| SCN | SCN normalization from Cournac 2012 |
| sim.other.methods | Compare other normalization methods on simulated data |
| sim_matrix | Simulate 2 Hi-C matrices with differences |
| sparse2full | Transform a sparse upper triangular matrix to a full Hi-C contact matrix |
| split_centromere | Function to split hic.table into 2 subsets at the centromere |
| total_sum | Total sum normalization for a list of hic.table objects |
| visualize_pvals | Function to visualize p-values from HiCcompare results |