HCT116_r1               A 4 column sparse matrix for a Hi-C matrix.
HCT116_r2               A 4 column sparse matrix for a Hi-C matrix.
HCT116_r3               A 4 column sparse matrix for a Hi-C matrix.
HCT116_r4               A 4 column sparse matrix for a Hi-C matrix.
HCT116_r5               A 4 column sparse matrix for a Hi-C matrix.
HCT116_r6               A 4 column sparse matrix for a Hi-C matrix.
Hicexp-class            An S4 class for working with Hi-C data
MD_composite            Plot a composite MD plot with the results of a
                        comparison
MD_hicexp               Make MD plots for all combinations of a
                        condition
cyclic_loess            Cyclic Loess normalization for Hi-C data
exportJuicebox          Export multiHiCcompare results for
                        visualization in Juicebox
fastlo                  Perform fast loess normalization on a Hi-C
                        experiment
hg19_cyto               A GenomicRanges object containing centromeric,
                        gvar, and stalk regions.
hg38_cyto               A GenomicRanges object containing centromeric,
                        gvar, and stalk regions.
hic_exactTest           Perform exact test based difference detection
                        on a Hi-C experiment
hic_filter              Perform filtering on a Hi-C experiment
hic_glm                 Function to perform GLM differential analysis
                        on Hi-C experiment
hic_scale               Perform library scaling on a hicexp object
hic_table               Print the hic_table
hicexp2                 hicexp object with 4 samples from two groups.
hicexp_diff             hicexp object with 7 samples from two groups.
make_hicexp             Make Hi-C experiment object from data
manhattan_hicexp        Manhattan plot function for results of
                        multiHiCcompare
meta                    Print the metadata
normalized              Print the indicator for if the data is
                        normalized
perm_test               Perform a permutation test to check enrichment
                        of a genomic feature with DIRs detected by
                        multiHiCcompare
plot_counts             Plot the count results from topDirs
plot_pvals              Plot the p-value results from topDirs
pval_heatmap            Function to visualize p-values from
                        multiHiCcompare results
resolution              Print the resolution
results                 Print the results
show,Hicexp-method      Print information about a HiCexp object
smartApply              Function to apply either biocParallel or
                        standard lapply
topDirs                 Filter results of multiHiCcompare
