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
HiCcompare-package      HiCcompare
KRnorm                  Performs KR (Knight-Ruiz) normalization on a
                        Hi-C matrix
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
SCN                     SCN normalization from Cournac 2012
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
hg19_blacklist          BED file for hg19 blacklisted regions
hg38_blacklist          BED file for hg38 blacklisted regions
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
hicpro2bedpe            Convert HiC-Pro results to BEDPE format
hmec.IS                 Hi-C data from HMEC cell line - chromosome 22
                        at 500kb resolution
make_InteractionSet     Convert HiCdiff results to InteractionSet
                        object
manhattan_plot          Create a Manhattan plot for the results of
                        HiCcompare
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
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
