# Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

## Documentation for package ‘multiHiCcompare’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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.
hg19_cyto | A GenomicRanges object containing centromeric, gvar, and stalk regions.
hg38_cyto | A GenomicRanges object containing centromeric, gvar, and stalk regions.
Hicexp-class | An S4 class for working with Hi-C data
hicexp2 | hicexp object with 4 samples from two groups.
hicexp_diff | hicexp object with 7 samples from two groups.
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
hic_table-method | Print the hic_table
make_hicexp | Make Hi-C experiment object from data
manhattan_hicexp | Manhattan plot function for results of multiHiCcompare
MD_composite | Plot a composite MD plot with the results of a comparison
MD_hicexp | Make MD plots for all combinations of a condition
meta | Print the metadata
meta-method | Print the metadata
normalized | Print the indicator for if the data is normalized
normalized-method | 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
resolution-method | Print the resolution
results | Print the results
results-method | Print the results
show-method | Print information about a HiCexp object
smartApply | Function to apply either biocParallel or standard lapply
topDirs | Filter results of multiHiCcompare