ChIPsim-package	ChIPsim-package
bindDens2readDens	bindDens2readDens
bindLocDens	distDens
ChIPsim	ChIPsim-package
decodeQuality	decodeQuality
defaultControl	defaultControl
defaultErrorProb	defaultErrorProb
defaultFunctions	defaultFunctions
defaultGenerator	defaultGenerator
defaultInit	defaultGenerator
defaultLastFeat	defaultGenerator
defaultTransition	defaultGenerator
distDens	distDens
encodeQuality	decodeQuality
extractQuality	extractQuality
feat2dens	feat2dens
featureDensity	featureDensity
featureDensity.FuzzyFeature	featureDensity
featureDensity.NFRFeature	featureDensity
featureDensity.ReversePhasedFeature	featureDensity
featureDensity.StableFeature	featureDensity
featureDensity.StablePhasedFeature	featureDensity
fragDens	distDens
fuzzyFeature	stableFeature
indNuc	distDens
joinRegion	joinRegion
makeFeatures	makeFeatures
nfrFeature	stableFeature
noNuc	distDens
phasedFeature	stableFeature
phaseNuc	distDens
placeFeatures	placeFeatures
pos2fastq	pos2fastq
readError	readError
readQualitySample	readQualitySample
readSequence	readSequence
reconcileFeatures	reconcileFeatures
reconcileFeatures.default	reconcileFeatures
reconcileFeatures.NucleosomePosition	reconcileFeatures
reconcileFeatures.SimulatedExperiment	reconcileFeatures
sampleFromFile	internal
sampleReads	sampleReads
simChIP	simChIP
simpleNames	simpleNames
solexaNames	internal
stableDens	distDens
stableFeature	stableFeature
writeFASTQ	writeFASTQ
writeIllumina	internal
writeReads	writeReads
