diffloop-package	diffloop
addchr	addchr
addchr,GRanges-method	addchr
addchr,loops-method	addchr
annotateAnchors	annotateAnchors
annotateAnchors,loops,GRanges,character,missing-method	annotateAnchors
annotateAnchors,loops,GRanges,character,numeric-method	annotateAnchors
annotateAnchors.bed	annotateAnchors.bed
annotateAnchors.bed,ANY-method	annotateAnchors.bed
annotateAnchors.bigwig	annotateAnchors.bigwig
annotateAnchors.bigwig,ANY-method	annotateAnchors.bigwig
annotateLoops	annotateLoops
annotateLoops,loops,GRanges,GRanges,GRanges-method	annotateLoops
annotateLoops,loops,missing,GRanges,GRanges-method	annotateLoops
annotateLoops.dge	annotateLoops.dge
annotateLoops.dge,ANY-method	annotateLoops.dge
bedToGRanges	bedToGRanges
bedToGRanges,character-method	bedToGRanges
calcLDSizeFactors	calcLDSizeFactors
calcLDSizeFactors,loops-method	calcLDSizeFactors
callCCDs	callCCDs
callCCDs,ANY-method	callCCDs
computeBoundaryScores	computeBoundaryScores
computeBoundaryScores,loops-method	computeBoundaryScores
diffloop	diffloop
dim,loops-method	dim-loops-method
featureTest	featureTest
featureTest,loops,GRanges-method	featureTest
filterLoops	filterLoops
filterLoops,ANY-method	filterLoops
filterSpanningLoops	filterSpanningLoops
filterSpanningLoops,loops,GRanges-method	filterSpanningLoops
geneinfo	geneinfo
getHumanGenes	getHumanGenes
getHumanGenes,character-method	getHumanGenes
getHumanGenes,missing-method	getHumanGenes
getHumanTSS	getHumanTSS
getHumanTSS,character-method	getHumanTSS
getHumanTSS,missing-method	getHumanTSS
getMouseGenes	getMouseGenes
getMouseGenes,character-method	getMouseGenes
getMouseGenes,missing-method	getMouseGenes
getMouseTSS	getMouseTSS
getMouseTSS,character-method	getMouseTSS
getMouseTSS,missing-method	getMouseTSS
head,loops-method	head-loops-method
human.genes	human.genes
interchromosomal	interchromosomal
interchromosomal,loops-method	interchromosomal
intrachromosomal	intrachromosomal
intrachromosomal,loops-method	intrachromosomal
keepCTCFloops	keepCTCFloops
keepCTCFloops,loops,GRanges-method	keepCTCFloops
keepEPloops	keepEPloops
keepEPloops,loops,GRanges,GRanges-method	keepEPloops
loopAssoc	loopAssoc
loopAssoc,loops-method	loopAssoc
loopDistancePlot	loopDistancePlot
loopDistancePlot,loops-method	loopDistancePlot
loopGenes	loopGenes
loopGenes,loops,GRanges-method	loopGenes
loopGenes,loops,missing-method	loopGenes
loopMetrics	loopMetrics
loopMetrics,loops-method	loopMetrics
loopPlot	loopPlot
loopPlot,loops,GRanges-method	loopPlot
loops	loops-class
loops-class	loops-class
loops.small	loops.small
loopsMake	loopsMake
loopsMake,ANY-method	loopsMake
loopsMake.mango	loopsMake.mango
loopsMake.mango,ANY-method	loopsMake.mango
loopsSubset	loopsSubset
loopsSubset,loops,loops-method	loopsSubset
loopWidth	loopWidth
loopWidth,loops-method	loopWidth
mangoCorrection	mangoCorrection
mangoCorrection,ANY-method	mangoCorrection
manyLoopPlots	manyLoopPlots
manyLoopPlots,loops,GRanges-method	manyLoopPlots
mergeAnchors	mergeAnchors
mergeAnchors,loops,numeric,logical-method	mergeAnchors
mergeAnchors,loops,numeric,missing-method	mergeAnchors
numAnchors	numAnchors
numAnchors,loops-method	numAnchors
numLoops	numLoops
numLoops,loops,missing-method	numLoops
numLoops,loops,numeric-method	numLoops
padGRanges	padGRanges
padGRanges,GRanges-method	padGRanges
pcaPlot	pcaPlot
pcaPlot,loops-method	pcaPlot
plotTopLoops	plotTopLoops
plotTopLoops,loops-method	plotTopLoops
quickAssoc	quickAssoc
quickAssoc,loops-method	quickAssoc
quickAssocVoom	quickAssocVoom
quickAssocVoom,loops-method	quickAssocVoom
removeRegion	removeRegion
removeRegion,loops,GRanges-method	removeRegion
removeSelfLoops	removeSelfLoops
removeSelfLoops,loops-method	removeSelfLoops
rmchr	rmchr
rmchr,GRanges-method	rmchr
rmchr,loops-method	rmchr
sampleNames,loops-method	sampleNames-loops-method
sampleNames<-,loops,ANY-method	sampleNames-loops-method
slidingWindowTest	slidingWindowTest
slidingWindowTest,loops,numeric,numeric-method	slidingWindowTest
splitSamples	splitSamples
splitSamples,loops-method	splitSamples
subsetLoops	subsetLoops
subsetLoops,loops,logical-method	subsetLoops
subsetLoops,loops,numeric-method	subsetLoops
subsetRegion	subsetRegion
subsetRegion,loops,GRanges,missing-method	subsetRegion
subsetRegion,loops,GRanges,numeric-method	subsetRegion
subsetRegionAB	subsetRegionAB
subsetRegionAB,loops,GRanges,GRanges-method	subsetRegionAB
summary,loops-method	summary-loops-method
tail,loops-method	tail-loops-method
topLoops	topLoops
topLoops,loops,missing,numeric-method	topLoops
topLoops,loops,numeric,missing-method	topLoops
topLoops,loops,numeric,numeric-method	topLoops
union,loops,loops-method	union-loops-loops-method
updateLDGroups	updateLDGroups
updateLDGroups,loops-method	updateLDGroups
[,loops,missing,numeric,missing-method	sub-loops-numeric-numeric-missing-method
[,loops,numeric,missing,missing-method	sub-loops-numeric-numeric-missing-method
[,loops,numeric,numeric,missing-method	sub-loops-numeric-numeric-missing-method
