$,pairParam-method	pairParam
annotatePairs	annotatePairs
boxPairs	boxPairs
clusterPairs	clusterPairs
compartmentalize	compartmentalize
connectCounts	connectCounts
consolidatePairs	consolidatePairs
correctedContact	correctedContact
cutGenome	cutGenome
diClusters	diClusters
diffHic	diffHicUsersGuide
diffHicUsersGuide	diffHicUsersGuide
domainDirections	domainDirections
emptyGenome	DNaseHiC
enrichedPairs	enrichedPairs
extractPatch	extractPatch
filterDiag	filterDiag
filterDirect	filters
filterPeaks	filterPeaks
filterTrended	filters
getArea	getArea
getPairData	getPairData
loadChromos	loadData
loadData	loadData
marginCounts	marginCounts
matchMargins	normalizeCNV
mergeCMs	mergeCMs
mergePairs	mergePairs
neighborCounts	neighborCounts
normalizeCNV	normalizeCNV
pairParam	pairParam
pairParam-class	pairParam
plotDI	plotDI
plotPlaid	plotPlaid
preparePairs	preparePairs
prepPseudoPairs	DNaseHiC
prunePairs	prunePairs
reform	pairParam
reform,pairParam-method	pairParam
rotDI	plotDI
rotPlaid	plotPlaid
savePairs	savePairs
segmentGenome	DNaseHiC
show,pairParam-method	pairParam
squareCounts	squareCounts
totalCounts	totalCounts
