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

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Documentation for package ‘HiCcompare’ version 1.30.0

• 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