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

brain_tableHi-C data from two regions of the brain at 100KB resolution
centromere_locationsLocations of the centromeres for hg19
coolerHi-C data in the cooler format
cooler2sparseTransform a .cool file to a sparse upper triangular matrix...
create.hic.tableCreate hic.table object from a sparse upper triangular Hi-C...
full2sparseTransfrom a full Hi-C contact matrix to a sparse upper...
get_CNVFunction to get the locations of copy number variations
hg19_blacklistBED file for hg19 blacklisted regions
hg38_blacklistBED file for hg38 blacklisted regions
HiCcompare-packageHiCcompare
hic_diffDetect differences between two jointly normalized Hi-C...
hic_loessPerform joint loess normalization on two Hi-C datasets
hicpro2bedpeConvert HiC-Pro results to BEDPE format
hic_simulateSimulate a Hi-C matrix and perform hic_diff analysis on it
HMEC.chr10Hi-C data from HMEC cell line - chromosome 10 at 500kb...
HMEC.chr22Hi-C data from HMEC cell line - chromosome 22 at 500kb...
hmec.ISHi-C data from HMEC cell line - chromosome 22 at 500kb...
KRnormPerforms KR (Knight-Ruiz) normalization on a Hi-C matrix
make_InteractionSetConvert HiCdiff results to InteractionSet object
MA_normPerform MA normalization on a hic.table object
MD.plot1Visualize the MD plot before and after loess normalization
MD.plot2Visualize the MD plot.
NHEK.chr10Hi-C data from NHEK cell line - chromosome 10 at 500kb...
NHEK.chr22Hi-C data from NHEK cell line - chromosome 22 at 500kb...
nhek.ISHi-C data from NHEK cell line - chromosome 22 at 500kb...
plot_Afunction to plot distribution of A to get input values for...
remove_centromereFunction to remove centromere columns and rows from a full...
SCNSCN normalization from Cournac 2012
sim.other.methodsCompare other normalization methods on simulated data
sparse2fullTransform a sparse upper triangular matrix to a full Hi-C...
split_centromereFunction to split hic.table into 2 subsets at the centromere
total_sumTotal sum normalization for a list of hic.table objects
visualize_pvalsFunction to visualize p-values from HiCcompare results
weight_MFunction to weight M values on the MD plot by Average...
HiCcompare documentation built on Nov. 17, 2017, 12:05 p.m.