$	DIList
$,DIList-method	DIList
$,pairParam-method	pairParam
anchors	DIList
anchors,DIList-method	DIList
asDGEList	DIList
asDGEList,DIList-method	DIList
boxPairs	boxPairs
c,DIList-method	DIList
clusterPairs	clusterPairs
colData	DIList
colData,DIList-method	DIList
connectCounts	connectCounts
consolidatePairs	consolidatePairs
correctedContact	correctedContact
counts	DIList
counts,DIList-method	DIList
cutGenome	cutGenome
diffHic	diffHicUsersGuide
diffHicUsersGuide	diffHicUsersGuide
DIList	DIList
DIList-class	DIList
dim,DIList-method	DIList
dimnames,DIList-method	DIList
enrichedPairs	enrichedPairs
exptData	DIList
exptData,DIList-method	DIList
filterDirect	filters
filterPeaks	filterPeaks
filterTrended	filters
getArea	getArea
getDistance	getDistance
getPairData	getPairData
loadChromos	loadData
loadData	loadData
marginCounts	marginCounts
matchMargins	normalizeCNV
mergePairs	mergePairs
normalize	DIList
normalize,DIList-method	DIList
normalizeCNV	normalizeCNV
pairParam	pairParam
pairParam-class	pairParam
plotDI	plotDI
plotPlaid	plotPlaid
preparePairs	preparePairs
prepPseudoPairs	DNaseHiC
prunePairs	prunePairs
reform	pairParam
reform,pairParam-method	pairParam
regions	DIList
regions,DIList-method	DIList
rotDI	plotDI
rotPlaid	plotPlaid
savePairs	savePairs
segmentGenome	DNaseHiC
show,DIList-method	DIList
show,pairParam-method	pairParam
squareCounts	squareCounts
targets	DIList
targets,DIList-method	DIList
totalCounts	totalCounts
[,DIList,ANY,ANY-method	DIList
