$,readParam-method	readParam
asDGEList	SEmethods
asDGEList,SummarizedExperiment-method	SEmethods
calculateCPM	calculateCPM
checkBimodality	checkBimodality
clusterFDR	clusterFDR
clusterWindows	clusterWindows
combineOverlaps	overlapStats
combineTests	combineTests
consolidateClusters	consolidateClusters
consolidateOverlaps	consolidateTests
consolidateSizes	consolidateWindows
consolidateTests	consolidateTests
consolidateWindows	consolidateWindows
controlClusterFDR	clusterFDR
correlateReads	correlateReads
csaw	csawUsersGuide
csawUsersGuide	csawUsersGuide
detailRanges	detailRanges
empiricalFDR	empiricalFDR
empiricalOverlaps	overlapStats
extractReads	extractReads
filterWindows	filterWindows
findMaxima	findMaxima
getBestOverlaps	overlapStats
getBestTest	getBestTest
getPESizes	getPESizes
getWidths	getWidths
maximizeCcf	maximizeCcf
mergeWindows	mergeWindows
mixedClusters	mixedClusters
mixedOverlaps	overlapStats
normFactors	normOffsets
normOffsets	normOffsets
profileSites	profileSites
readParam	readParam
readParam-class	readParam
reform	readParam
reform,readParam-method	readParam
regionCounts	regionCounts
scaleControlFilter	filterWindows
scaledAverage	scaledAverage
show,readParam-method	readParam
strandedCounts	strandedCounts
summitOverlaps	overlapStats
upweightSummit	upweightSummit
windowCounts	windowCounts
wwhm	wwhm
