# HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

## Documentation for package ‘HiCcompare’ version 1.29.0

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

## Help Pages

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
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